Development of a hypoxia-responsive vector for tumor-specific gene therapy.
We are developing new gene therapy vectors whose expression is selectively activated by hypoxia, a unique feature of human solid tumors. As vascular endothelial growth factor (VEGF) is upregulated by hypoxia, such regulatory mechanisms would enable us to achieve hypoxia-inducible expression of therapeutic genes. Constructs with five copies of hypoxia-responsive elements (HREs) derived from the 5'-untranslated region (UTR) of the human VEGF showed excellent transcriptional activation at low oxygen tension relevant to tumor hypoxia. In an attempt to achieve higher responsiveness, various combinations of HREs and promoters were examined. In addition, we also investigated whether the 3' UTR of the VEGF gene would confer increased post-transcriptional mRNA stability under hypoxic conditions. However, despite increases in the hypoxic/aerobic ratio of luciferase activity, gene expression with 3' UTR was lower due to mRNA destabilization by AU-rich elements (AREs). Thus, we found no benefit from the inclusion of the 3' UTR in our vectors. Of all the vectors tested, the combination of 5HRE and a CMV minimal promoter exhibited hypoxia responsiveness (over 500-fold) to the similar level to the intact CMV promoter. We propose that this vector would be useful for tumor selective gene therapy.


Rediscovery of the type series of the Sacred Shrew, Sorex religiosus I. Geoffroy Saint-Hilaire, 1826, with additional notes on mummified shrews of ancient Egypt (Mammalia: Soricidae).
In 1826, Isidore Geoffroy Saint-Hilaire described the Sacred Shrew, Sorex religiosus [= Crocidura religiosa] from a series of 22 embalmed individuals that comprised a portion of the Italian archeologist Joseph Passalacqua's collection of Egyptian antiquities from an ancient necropolis near Thebes, central Egypt. Living members of the species were not discovered until the beginning of the 20th century and are currently restricted to the Nile Delta region, well north of the type locality. In 1968, the type series of S. religiosus was reported lost, and in 1978, a neotype was designated from among a small collection of modern specimens in the Natural History Museum, London. Our investigations have revealed, however, that the type series is still extant. Most of the specimens used by I. Geoffroy Saint-Hilaire to describe S. religiosus still form part of the Passalacqua Collection in the Ägyptisches Museum, Berlin, Germany. We summarize the taxonomic history of S. religiosus, review the history of the Passalacqua collection, and explain why the type series was thought to have been lost. We designate an appropriate lectotype from among the original syntypes of S. religiosus in the Ägyptisches Museum. Our examination of the shrew mummies in the Passalacqua collection also yielded a species previously unrecorded from either ancient or modern Egypt: Crocidura pasha Dollman, 1915. Its presence increases the number of soricid species embalmed in ancient Egypt to seven and provides additional evidence for a more diverse Egyptian shrew fauna in the archeological past. Finally, we provide details that will assist in better understanding the variety of mummification procedures used to preserve animals in ancient Egypt.


Scientific Utopia III: Crowdsourcing Science.
Most scientific research is conducted by small teams of investigators who together formulate hypotheses, collect data, conduct analyses, and report novel findings. These teams operate independently as vertically integrated silos. Here we argue that scientific research that is horizontally distributed can provide substantial complementary value, aiming to maximize available resources, promote inclusiveness and transparency, and increase rigor and reliability. This alternative approach enables researchers to tackle ambitious projects that would not be possible under the standard model. Crowdsourced scientific initiatives vary in the degree of communication between project members from largely independent work curated by a coordination team to crowd collaboration on shared activities. The potential benefits and challenges of large-scale collaboration span the entire research process: ideation, study design, data collection, data analysis, reporting, and peer review. Complementing traditional small science with crowdsourced approaches can accelerate the progress of science and improve the quality of scientific research.


Jordanian physicians' perceived barriers and facilitators to patient participation in treatment decision-making: An exploratory study.
Successful implementation of shared decision-making in clinical encounters is influenced by system, patient, and clinician factors that both facilitate and present barriers to patient-centered care. Little is known about which factors Jordanian physicians believe influence their ability to implement shared decision-making with cancer patients. To determine Jordanian physicians' perceived barriers and facilitators to patient participation in treatment decision-making. A cross-sectional exploratory survey design was used in the study. A convenience sample of 86 Jordanian medical and radiation oncologists and surgeons was recruited. A valid measure of physicians' views of shared decision-making was slightly modified from its original English and used to collect data. Data were analyzed using the Statistical Package for the Social Sciences (SPSS) for windows version 19.0 (SPSS, Inc., Chicago, IL, USA). Descriptive and inferential statistics were carried as appropriate. Insufficient time to spend with the patient, patient expecting a certain treatment rather than a consultation, and the patient's family overriding the decision-making process were the most frequently reported barriers to patient participation in treatment decision-making. Physicians believed that patients trust in physicians and patient being accompanied at the consultation were important facilitators of patient participation in treatment decision-making. Jordanian physicians perceive multiple barriers to patient participation in treatment decision-making. Patient-related difficulties (e.g., indecision), and system-related difficulties, in particular, patient's family influence on the decision-making process are more prevalent among Jordanian physicians compared to Western physicians.


Expression of bone morphogenetic proteins in human prostatic adenocarcinoma and benign prostatic hyperplasia.
There are important interactions between prostatic tumours and bone. This study was designed to examine whether prostatic tissue can express bone inductive factors, in particular, the Bone Morphogenetic Proteins (BMPs). The polymerase chain reaction (PCR) has been used to screen for the expression of BMPs one to six in the prostatic tissue of patients with benign prostatic hyperplasia (BPH), non-metastatic prostatic adenocarcinoma and metastatic prostatic adenocarcinoma. BMPs were expressed in both benign and malignant prostate tissue and in the prostate tumour cell lines, PC3 and DU145. BMPs were also expressed in ocular melanoma tissue, a tissue which rarely metastasizes to bone. BMP-6 expression was detected in the prostate tissue of over 50% of patients with clinically defined metastatic prostate adenocarcinoma, but was not detected in non-metastatic or benign prostate samples or in ocular melanoma tissue. These findings suggest that the BMPs may play a role in the osteoinductive activity of prostate metastases and that the pattern of expression of BMPs may be important in the pathogenesis of osteoblastic metastases associated with prostate adenocarcinoma.


Pivotal role of inosine triphosphate pyrophosphatase in maintaining genome stability and the prevention of apoptosis in human cells.
Pure nucleotide precursor pools are a prerequisite for high-fidelity DNA replication and the suppression of mutagenesis and carcinogenesis. ITPases are nucleoside triphosphate pyrophosphatases that clean the precursor pools of the non-canonical triphosphates of inosine and xanthine. The precise role of the human ITPase, encoded by the ITPA gene, is not clearly defined. ITPA is clinically important because a widespread polymorphism, 94C>A, leads to null ITPase activity in erythrocytes and is associated with an adverse reaction to thiopurine drugs. We studied the cellular function of ITPA in HeLa cells using the purine analog 6-N hydroxylaminopurine (HAP), whose triphosphate is also a substrate for ITPA. In this study, we demonstrate that ITPA knockdown sensitizes HeLa cells to HAP-induced DNA breaks and apoptosis. The HAP-induced DNA damage and cytotoxicity observed in ITPA knockdown cells are rescued by an overexpression of the yeast ITPase encoded by the HAM1 gene. We further show that ITPA knockdown results in elevated mutagenesis in response to HAP treatment. Our studies reveal the significance of ITPA in preventing base analog-induced apoptosis, DNA damage and mutagenesis in human cells. This implies that individuals with defective ITPase are predisposed to genome damage by impurities in nucleotide pools, which is drastically augmented by therapy with purine analogs. They are also at an elevated risk for degenerative diseases and cancer.


Multimode all-fiber quasi-distributed refractometer sensor array and cross-talk mitigation.
The analysis and design of a quasi-distributed multimode fiber refractometer array is presented. The main challenge in the design of a practical quasi-distributed sensor array proved to be in mitigation of otherwise pronounced cross-talk effects among the individual sensors in the network. The cross-talk effects originate from mode filtering properties and the strong mode excitation dependence on the multimode refractometer sensors that constitute the array. The introduction of mode conditioning based on fiber mode filters and mode mixers effectively reduced the cross talk to a negligible level while providing the desired sensor response at acceptable collateral losses to the network. A comprehensive experimental analysis was carried out to provide detailed insight into the multimode sensor array behavior and to obtain data necessary for an overall and effective network design.


Effects of UGT2B7, SCN1A and CYP3A4 on the therapeutic response of sodium valproate treatment in children with generalized seizures.
This study aims to evaluate the associations between genetic polymorphisms and the effect of sodium valproate (VPA) therapy in children with generalized seizures. A total of 174 children with generalized seizures on VPA therapy were enrolled. Steady-state trough plasma concentrations of VPA were analyzed. Seventy-six single nucleotide polymorphisms involved in the absorption, metabolism, transport, and target receptor of VPA were identified, and their associations with the therapeutic effect (seizure reduction) were evaluated using logistic regression adjusted by various influence factors. rs7668282 (UGT2B7, T > C, OR = 2.67, 95% CI: 1.19 to 5.91, P = 0.017) was more prevalent in drug-resistant patients than drug-responsive patients. rs2242480 (CYP3A4, C > T, OR = 0.27, 95% CI: 0.095 to 0.79, P = 0.017) and rs10188577 (SCN1A, T > C, OR = 0.40, 95% CI: 0.17 to 0.94, P = 0.035) were more prevalent in drug-responsive patients compared to drug-resistant patients. In children with generalized seizures on VPA therapy, polymorphisms of UGT2B7, CYP3A4, and SCN1A genes were associated with seizure reduction. Larger studies are warranted to corroborate the results.


Optimised uncertainty in food analysis: application and comparison between four contrasting 'analyte-commodity' combinations.
The optimised uncertainty (OU) methodology is applied across a range of analyte-commodity combinations. The commodities and respective analytes under investigation were chosen to encompass a range of input factors: measurement costs (sampling and analytical), sampling uncertainties, analytical uncertainties and potential consequence costs which may be incurred as a result of misclassification. Two types of misclassification are identified-false compliance and false non-compliance. These terms can be used across a wide range of foodstuffs that have regulations requiring either minimum compositional requirements, maximum contaminant allowances or compositional specifications. The latter refers to foodstuffs with regulations that state an allowable tolerance around the compositional specification, i.e. the upper specification limit (USL) and the lower specification limit (LSL). The traditional OU methodology has been adapted so that it is applicable in these cases and has been successfully applied in practice. The Newton-Raphson method has been used to determine the optimal uncertainty value for the two case studies in which analyte concentration is assessed against a 'single threshold' regulatory requirement. This numerical method was shown to give a value of the optimal uncertainty that is practically identical to that given by the previously used method of visual inspection. The expectation of financial loss was reduced by an average of 65% over the four commodities by the application of the OU methodology, showing the benefit of the method.


Col1A-2 Mutation in Osteogenesis Imperfecta Mice Contributes to Long Bone Fragility by Modifying Cell-Matrix Organization.
Osteogenesis imperfecta (OI) is a rare congenital bone dysplasia generally caused by a mutation of one of the type I collagen genes and characterized by low bone mass, numerous fractures, and bone deformities. The collagen organization and osteocyte lacuna arrangement were investigated in the long bones of 17-week-old wildtype (WT, n = 17) and osteogenesis imperfecta mice (OIM, n = 16) that is a validated model of severe human OI in order to assess their possible role in bone fragility. Fractures were counted after in vivo scanning at weeks 5, 11, and 17. Humerus, femur, and tibia diaphyses from both groups were analyzed ex vivo with pQCT, polarized and ordinary light histology, and Nano-CT. The fractures observed in the OIM were more numerous in the humerus and femur than in the tibia, whereas the quantitative bone parameters were altered in different ways among these bones. Collagen fiber organization appeared disrupted, with a lower birefringence in OIM than WT bones, whereas the osteocyte lacunae were more numerous, more spherical, and not aligned in a lamellar pattern. These modifications, which are typical of immature and less mechanically competent bone, attest to the reciprocal alteration of collagen matrix and osteocyte lacuna organization in the OIM, thereby contributing to bone fragility.


Inhibition of myeloid differentiation by the helix-loop-helix protein Id.
Id is a helix-loop-helix (HLH) protein that represses activity of several basic helix-loop-helix (bHLH) proteins involved in cell type--specific transcription and cell lineage commitment. The myeloid precursor cell line 32DC13(G) expressed Id messenger RNA, which was transiently decreased when cells were induced to terminally differentiate with granulocyte--colony-stimulating factor. Concomitant with the decrease of Id messenger RNA was the appearance in nuclear extracts of DNA binding proteins that recognized a canonical E-box motif, a DNA binding site for some bHLH proteins. Constitutive expression of an Id complementary DNA in 32DC13(G) cells blocked their ability to differentiate and to induce E-box-binding activity. These results suggest that Id and, hence, bHLH proteins function in the process of myeloid differentiation.


Anthropogenic- and natural sources of dust in peatland during the Anthropocene.
As human impact have been increasing strongly over the last decades, it is crucial to distinguish human-induced dust sources from natural ones in order to define the boundary of a newly proposed epoch - the Anthropocene. Here, we track anthropogenic signatures and natural geochemical anomalies in the Mukhrino peatland, Western Siberia. Human activity was recorded there from cal AD 1958 (±6). Anthropogenic spheroidal aluminosilicates clearly identify the beginning of industrial development and are proposed as a new indicator of the Anthropocene. In cal AD 1963 (±5), greatly elevated dust deposition and an increase in REE serve to show that the geochemistry of elements in the peat can be evidence of nuclear weapon testing; such constituted an enormous force blowing soil dust into the atmosphere. Among the natural dust sources, minor signals of dryness and of the Tunguska cosmic body (TCB) impact were noted. The TCB impact was indirectly confirmed by an unusual occurrence of mullite in the peat.


dRYBP contributes to the negative regulation of the Drosophila Imd pathway.
The Drosophila humoral innate immune response fights infection by producing antimicrobial peptides (AMPs) through the microbe-specific activation of the Toll or the Imd signaling pathway. Upon systemic infection, the production of AMPs is both positively and negatively regulated to reach a balanced immune response required for survival. Here, we report the function of the dRYBP (drosophila Ring and YY1 Binding Protein) protein, which contains a ubiquitin-binding domain, in the Imd pathway. We have found that dRYBP contributes to the negative regulation of AMP production: upon systemic infection with Gram-negative bacteria, Diptericin expression is up-regulated in the absence of dRYBP and down-regulated in the presence of high levels of dRYBP. Epistatic analyses using gain and loss of function alleles of imd, Relish, or skpA and dRYBP suggest that dRYBP functions upstream or together with SKPA, a member of the SCF-E3-ubiquitin ligase complex, to repress the Imd signaling cascade. We propose that the role of dRYBP in the regulation of the Imd signaling pathway is to function as a ubiquitin adaptor protein together with SKPA to promote SCF-dependent proteasomal degradation of Relish. Beyond the identification of dRYBP as a novel component of Imd pathway regulation, our results also suggest that the evolutionarily conserved RYBP protein may be involved in the human innate immune response.


Heart rates of northern elephant seals diving at sea and resting on the beach.
Heart rates of northern elephant seals diving at sea and during apnoea on land were monitored to test whether a cardiac response to submergence is an important factor in their ability to make repetitive, long-duration dives. Seven juvenile northern elephant seals were captured at Año Nuevo, CA, instrumented and translocated to release sites around Monterey Bay. Heart rate and dive depth were recorded using custom-designed data loggers and analogue tape monitors during the seals' return to Año Nuevo. Heart rates during apnoea and eupnoea were recorded from four of the seals after they hauled out on the beach. Diving patterns were very similar to those of naturally migrating juveniles. The heart rate response to apnoea at sea and on land was a prompt bradycardia, but only at sea was there an anticipatory tachycardia before breathing commenced. Heart rate at sea declined by 64% from the surface rate of 107 +/- 3 beats min-1 (mean +/- S.D.), while heart rate on land declined by 31% from the eupnoeic rate of 65 +/- 8 beats min-1. Diving heart rate was inversely related to dive duration in a non-linear fashion best described by a continuous, curvilinear model, while heart rate during apnoea on land was independent of the duration of apnoea. Occasionally, instantaneous heart rate fell as low as 3 beats min-1 during diving. Although bradycardia occurs in response to apnoea both at sea and on land, only at sea is heart rate apparently regulated to minimise eupnoeic time and to ration oxygen stores to ensure adequate supplies for the heart and brain not only as the dive progresses normally but also when a dive is abnormally extended.


Anti-apoptotic properties of Ginkgo biloba extract EGb 761 in differentiated PC12 cells.
Standard Ginkgo biloba leaf extract (EGb 761) has been known to have neuroprotective effects ranging from molecular and cellular, to animal and human studies, however, the cellular and molecular mechanisms remain unclear. Using PC 12 cells, a well-established model for studying neuroprotection, we have determined the mechanism of action of EGb 761 on cell survival following apoptosis induced by serum-deprivation or treatment with staurosporine (STS). Our results show that EGb 761 treatments of PC12 cells are able to prevent serum deprivation- and STS-induced mitochondrial damage, attenuate release of cytochrome c and DNA fragmentation. EGb 761, but not vitamin E. inhibited STS-induced activation of the caspase-3 enzyme. Two of the EGb 761 components, bilobalide B and ginkgolide C show more significant inhibition than the EGb 761 extract. Furthermore, DNA microarray assay results indicate that transcription of multiple apoptosis-related genes is either up- or down-regulated in cells treated with EGb 761. These results suggest that inhibition of apoptotic machinery may, at least in part, mediate multiple neuroprotective effects of EGb 761, and that EGb 761 and vitamin E act on different molecular paths to provide neuroprotection.


Allelic variation of a Beauveria bassiana (Ascomycota: Hypocreales) minisatellite is independent of host range and geographic origin.
The minisatellite locus, BbMin1, was isolated from a partial Beauveria bassiana genomic library that consisted of poly(GA) flanked inserts. Polymerase chain reaction (PCR) of the BbMin1 repeat demonstrated allele size variation among 95 B. bassiana isolates. Amplification was also observed from single isolates of Beauveria amorpha, Beauveria brongniartii, and Beauveria caledonica. Eight alleles were identified at the haploid locus, where repeat number fluctuated between one and fourteen. AMOVA and theta (Fst) indicated that fixation of repeat number has not occurred within pathogenic ecotypes or geographically isolated samples of B. bassiana. Selective neutrality of allele size, the rate of BbMin1 mutation, and the age of the species may contribute to host and geographic independence of the marker. Presence of alleles with a large number of repeat units may be attributed to the rare occurrence of somatic recombination or DNA replication error. The molecular genetic marker was useful for the identification of genetic types of B. bassiana and related species.


Obesity, outcomes and quality of care: body mass index increases the risk of wound-related complications in colon cancer surgery.
Obese patients may face higher complication rates during surgical treatment of colon cancer. The aim of this study was to measure this effect at a high-volume tertiary care center. All patients with colon cancer treated surgically at a single center from 2004 through 2011 were reviewed. Multivariate regression assessed relationships of complications and stay outcomes with body mass index (BMI) controlling for age, gender, comorbidity score, surgical approach, and history of smoking. In 1,048 included patients, BMI was a predictor of several complications in both laparoscopic and open procedures. For every increase of BMI by one World Health Organization category, the odds ratios were 1.61 (P < .001) for wound infection and 1.54 (P < .001) for slow healing. Additionally, right colectomies had an odds ratio of 3.23 (P = .017) for wound dehiscence. No further associations with BMI were found. BMI was incrementally associated with wound-related complications, illustrating how the proliferation of obesity relates to a growing risk for surgical complications. As the surgical community strives to improve the quality of care, patient-controllable factors will play an increasingly important role in cost containment and quality improvement.


Colletotrichum lindemuthianum Races Prevalent on Dry Beans in North Dakota and Potential Sources of Resistance.
Anthracnose caused by Colletotrichum lindemuthianum is one of the most important diseases of dry edible beans in the major production areas worldwide. This pathogen is highly variable, with numerous races. Disease management relies heavily on genetic resistance and use of clean seed. Genetic resistance is controlled by major resistance genes conferring protection against specific races of the pathogen. Therefore, knowledge of the pathogen population in a region is essential for effective screening of germplasm. Surveys were conducted for more than 6 years in North Dakota, the largest dry-bean-growing state in the United States, and seed samples submitted for certification were assessed to identify the C. lindemuthianum races prevalent in the region. A collection of commercial cultivars from different market classes of dry bean was also screened for resistance to these races. Disease incidence was found to be low in most years. However, in addition to the previously reported races of anthracnose 7, 73, and 89, two new races, 1153 and 1161, previously never reported in the United States, were identified and the commercial cvs. Montcalm, Avalanche, Vista, and Sedona where found to possess resistance to these races.


Human Cytomegalovirus interleukin-10 promotes proliferation and migration of MCF-7 breast cancer cells.
Breast cancer is the most common malignancy affecting women worldwide. While a small fraction of breast cancers have a hereditary component, environmental and behavioral factors also impact the development of cancer. Human cytomegalovirus (HCMV) is a member of the Herpesviridae family that is widespread in the general population and has been linked to several forms of cancer. While HCMV DNA has been found in some breast cancer tissue specimens, we wanted to investigate whether a secreted viral cytokine might have an effect on cancerous or even pre-cancerous cells. HCMV encodes an ortholog of the human cellular cytokine interleukin-10 (IL-10). The HCMV UL111A gene product is cmvIL-10, which has 27% sequence identity to IL-10 and binds the cellular IL-10 receptor (IL-10R) to induce downstream cell signaling. We found that MCF-7 human breast cancer cells express IL-10R and that exposure to cmvIL-10 results in enhanced proliferation and increased chemotaxis of MCF-7 cells. PCR arrays revealed that treatment with cmvIL-10 alters expression of cell adhesion molecules and increases MMP gene expression. In particular, MMP-10 gene expression was found to be significantly up-regulated and this correlated with an increase in cell-associated MMP-10 protein produced by MCF-7 cells exposed to cmvIL-10. These results suggest that the presence of cmvIL-10 in the tumor microenvironment could contribute to the development of more invasive tumors.


Mood and anxiety disorders following pediatric traumatic brain injury: a prospective study.
Studies utilizing standardized instruments for assessing mood and/or anxiety disorders following pediatric traumatic brain injury have seldom been reported in the literature. Previous reports have largely focused on cognitive impairment, behavioral dysfunction, or adaptive functioning, and have typically relied on parental informants. In this study, children hospitalized for mild (N = 42) and moderate/severe (N = 19) brain injury were assessed 6-months postinjury using the Anxiety disorders Module A and the Mood disorders Module C of the Diagnostic Interview Schedule for Children - IV Revision (DISC-IV). The data collected for the brain injury groups were compared to an orthopedic control group (N = 35). The relationship between a new onset mood and/or anxiety disorder (NOD) and injury severity indices was examined. Sequential logistical regression was also utilized to examine the impact of a brain injury, demographic variables, preinjury psychiatric disturbance, development disorders, litigation status and postinjury environmental stress on emotional outcome. Results indicated a relationship between brain injury and NOD. Multivariate analysis demonstrated that postinjury level of stress and severity of brain injury were the most robust predictors of NOD, accounting for 23% of the variance in the model. These results support the premise that the development of a mood and/or anxiety disorder following pediatric head injury is mediated by multiple determinants. The findings suggest that early psychosocial assessment and interventions aimed at increasing a child's coping may attenuate the emotional consequences of pediatric brain injury.


Colonoscopy in France during the COVID-19 pandemic.
We hypothesized that the COVID-19 pandemic may have modified dispensing of colonoscopy preparations, a proxy for the number of colonoscopies performed. We therefore studied changes in dispensing of colonoscopy preparations during the pandemic in France. Using the French national health data system, we identified colonoscopy preparations dispensed from 2018 to 2020. The expected 2020 dispensations were estimated from 2018 to 2019 dispensations. Dispensing of colonoscopy preparations decreased markedly during the eight weeks of national lockdown: 83,045 colonoscopy preparations were dispensed, i.e., 181,826 (68.6%) fewer than expected. After lockdown, dispensing of colonoscopy preparations gradually returned to expected numbers. Overall, this represents an estimated decrease of roughly 250,000 colonoscopy preparations during the six-month period following onset of the pandemic. This shortfall in the dispensing of colonoscopy preparations was of the same order of magnitude in people under or over 50 years of age, in men and women, and in those in the highest and the lowest quintiles of the deprivation index. In conclusion, roughly 250,000 fewer colonoscopy preparations were dispensed during the first six months of the COVID-19 pandemic in France. Deleterious consequences on morbidity and mortality related to gastroenterological diseases, such as colorectal cancer, are to be feared.


Cortical-like dynamics in recurrent circuits optimized for sampling-based probabilistic inference.
Sensory cortices display a suite of ubiquitous dynamical features, such as ongoing noise variability, transient overshoots and oscillations, that have so far escaped a common, principled theoretical account. We developed a unifying model for these phenomena by training a recurrent excitatory-inhibitory neural circuit model of a visual cortical hypercolumn to perform sampling-based probabilistic inference. The optimized network displayed several key biological properties, including divisive normalization and stimulus-modulated noise variability, inhibition-dominated transients at stimulus onset and strong gamma oscillations. These dynamical features had distinct functional roles in speeding up inferences and made predictions that we confirmed in novel analyses of recordings from awake monkeys. Our results suggest that the basic motifs of cortical dynamics emerge as a consequence of the efficient implementation of the same computational function-fast sampling-based inference-and predict further properties of these motifs that can be tested in future experiments.


Treatment of hydrogen molecule abates oxidative stress and alleviates bone loss induced by modeled microgravity in rats.
Treatment with molecular hydrogen alleviates microgravity-induced bone loss through abating oxidative stress, restoring osteoblastic differentiation, and suppressing osteoclast differentiation and osteoclastogenesis. Recently, it has been suggested that hydrogen gas exerts a therapeutic antioxidant activity by selectively reducing cytotoxic reactive oxygen species (ROS). The aim of the present study was to elucidate whether treatment with molecular hydrogen alleviated bone loss induced by modeled microgravity in rats. Hindlimb suspension (HLS) and rotary wall vessel bioreactor were used to model microgravity in vivo and in vitro, respectively. Sprague-Dawley rats were exposed to HLS for 6 weeks to induced bone loss and simultaneously administrated with hydrogen water (HW). Then, we investigated the effects of incubation with hydrogen-rich medium (HRM) on MC3T3-E1 and RAW264.7 cells exposed to modeled microgravity. Treatment with HW alleviated HLS-induced reduction of bone mineral density, ultimate load, stiffness, and energy in femur and lumbar vertebra. Treatment with HW alleviated HLS-induced augmentation of malondialdehyde content and peroxynitrite content and reduction of total sulfhydryl content in femur and lumbar vertebra. In cultured MC3T3-E1 cells, incubation with HRM inhibited modeled microgravity-induced ROS formation, reduction of osteoblastic differentiation, increase of ratio of receptor activator of nuclear factor kappa B ligand to osteoprotegerin, inducible nitric oxide synthetase upregulation, and Erk1/2 phosphorylation. In cultured RAW264.7, incubation with HRM aggravated modeled microgravity-induced ROS formation, osteoclastic differentiation, and osteoclastogenesis. Treatment with molecular hydrogen alleviates microgravity-induced bone loss in rats. Molecular hydrogen could thus be envisaged as a nutritional countermeasure for spaceflight but remains to be tested in humans.


RBL-2H3 cells are an imprecise model for mast cell mediator release.
The cell line, RBL-2H3, has been widely used as a mast cell model though much of the data is contradictory. The aim of this study is to assess the RBL-2H3 cell line as an in vitro model for degranulation studies. RBL-2H3 cells were stimulated with either dinitrophenylated-IgE, calcium ionophore A23187, compound 48/80, mast cell degranulating peptide or lipopolysaccharide and mediator (histamine, beta-hexosaminidase, interleukin-13 and TNF-alpha) release was analysed. Toll-like receptors (TLR) mRNA expression in RBL-2H3 cells and rat peritoneal mast cells (RPMC) were compared by RT-PCR. TLR4 and CD14 surface proteins in RBL-2H3 were analysed by FACS. Mediator release was dependent on media composition and degranulation was stimulated by IgE and A23187. Degranulation was inhibited by quercetin, but not by cromoglycate or ketotifen. Transcripts encoding TLR3-5 and 6 were detected in RBL-2H3 cells whereas TLR1-6 and TLR8 were clearly seen in RPMC. While proteins were detected for TLR4 in RBL-2H3 cells, CD14 was largely absent. While RBL-2H3 cells may be useful as a model for mast cell IgE-mediated degranulation, other aspects may not be representative and they may share similarities with basophils rather than with other histamine-releasing cell types.


Eating behaviour patterns in Chinese children aged 12-18 months and association with relative weight--factorial validation of the Children's Eating Behaviour Questionnaire.
Eating behaviours have been suggested relating to obesity development. The Children's Eating Behaviour Questionnaire (CEBQ) is a parent-report measure constructed to assess multiple dimensions of eating behavior for children. This study aimed to test the validity of the Chinese version of Children's Eating Behaviour Questionnaire (CEBQ) in Chinese children aged 12-18 months. We examined factor structure and the reliability of the Chinese version of the CEBQ, the associations between children's eating behaviours and children's weight (BMI SDS) were assessed. 219 questionnaires were filled out by the caregivers, approached in community health care centers in two cities in China. BMI of each child was calculated and converted to BMI SDS. Factor validation (Principal Component Analysis, exploratory factor analysis) on all CEBQ items was performed and gender difference in eating behaviours was examined. Correlations between eating behaviours and the child's BMI SDS were analyzed by linear regression analysis controlling for gender, parental combined weight, and education. The factor analysis revealed a seven-factor solution, with factor 'food responsiveness' (FR) split into two. 'Satiety responsiveness' (SR) and 'Enjoyment of food' (EF) factors were not detected. Interestingly, boys scored higher than girls in the FR scales, whereas girls had a higher score in 'food fussiness' (FF) scale. We conclude that although a valuable psychometric instrument, CEBQ might be affected by age and cultural differences. Therefore, adjusting it in order to fit the Chinese population was suggested. We did not find an association between eating behaviours and children's BMI SDS, when it was controlled for gender and parental weight.


Concentrations of chlorinated pollutants in adipose tissue of yellow-legged gulls (Larus michahellis) from Spain: Role of gender and age.
Concentrations of 7 different polychlorinated biphenyl (PCB) congeners, and eleven organochlorine pesticides (OCPs) and metabolites, including DDTs (dichlorodiphenyltrichloroethane), HCHs (hexachlorocyclohexane isomers), Endosulfan, Endosulfan sulfate, Endrin, Dieldrin and HCB (hexachlorobenzene), were determined in adipose tissue of 57 yellow-legged gulls collected from NW and N Spain. Furthermore, the possible differences due to two endogenous factors, age and gender, were determined. All the analyzed PCBs were detected in over 66% of the samples, with levels of 291.9 (PCB 180), 34.5 (PCB 118), 0.7 (PCB 28), 432.6 (PCB 153), 225.5 (PCB 138), 1.3 (PCB 101) and 0.4 (PCB 52) µg/kg of adipose tissue. With respect to the OCPs and metabolites, only 4,4'-DDE and HCB were detected in more than 50% of the samples, with means of 360.6 and 2.5 µg/kg of adipose tissue, respectively. From all the considered contaminants, only 4,4'-DDE levels presented significant differences depending on the gender, with females showing higher values than males (p < 0.01). Significant differences (p < 0.001) were also found related to age for the levels of PCBs 180, 138, 101, 28 and 153, as well as 4,4'-DDE, with adult levels being higher than those in young birds. The results of the present study constitute a baseline to better assess the environmental impacts of PCB and OCP contamination at other coastal sites for future biomonitoring studies, with particular emphasis on gender- and age-related differences.


A new mitochondrial C1 lineage from the prehistory of Uruguay: population genocide, ethnocide, and continuity.
Uruguayan population has been considered as of European descent, as its Native populations victims of genocide apparently disappeared in the 19th century. Contradicting this national belief, genetic studies have shown a substantial Native contribution. However, the continuity between prehistoric, historic, and present populations remains unproved. With the aim of adding elements to prove a possible population continuity, we studied a mitochondrial lineage, part of haplogroup C1, analyzing the complete genome of a modern Uruguayan individual and the hypervariable region I (HVRI) in prehistoric, historic, and contemporary individuals. Several individuals carried the mutations that characterize this lineage: two from an archaeological mound located in the east of the country, the Charrúa Indian chief Vaimaca Perú and five individuals from the present population. The lineage was initially characterized by its HVRI sequence, having the four typical C1 mutations and adding 16051G and 16288C; other mutations were also found: 16140C was found in all but the oldest individual, dated 1,610 years BP, while 16209C, 16422C, and 16519C were found only in some individuals. Hypervariable region II showed the typical C1 mutations and 194T. The coding region, analyzed in modern individuals, was characterized by 12378T, while other mutations found were not common to all of them. In summary, we have found and described a new lineage that shows continuity from prehistoric mound builders to the present population, through a representative of the extinct Charrúa Indians. The lineage appeared at least 1,600 years ago and is carried by approximately 0.7% of the modern Uruguayan population. The continuity of the lineage supports alternative perspectives about Uruguayan national identity and the meaning of the genocide, best labeled as ethnocide because of its consequences. It also contributes to the discussion about who the prehistoric mound builders were, and to the origin, at least in the maternal line, of a Charrúa Indian. From a more general perspective, we can conclude that the characteristics, evolution, and expansion of founder haplogroup C in America have not yet been elucidated.


Molecular dynamics simulations applied to electric field induced second harmonic generation in dipolar chromophore solutions.
Electric field induced second harmonic generation (EFISH) is an important experimental technique in extracting the first hyperpolarizability of an organic chromophore molecule. Such experiments are carried out in solutions with chromophore molecules dissolved in some common solvents. A known fact is that the first hyperpolarizabilities extracted from EFISH experiments are subject to the use of local field factors. In this work, we apply simulations to study the EFISH properties of chromophore solutions. By combining quantum chemistry calculations with the results derived from molecular dynamics simulations, we show how macroscopic EFISH properties can be modeled, using 4-(dimethylamino)-4'-nitroazobenzene dissolved in chloroform as a demonstration case. The focus of the study is on deriving accurate local field factors. We find that the local field approach applies very well to dipolar solutions, such as the one studied here, but that the local field factors derived are much smaller than the commonly used Onsager or Lorentz local field factors. Our study indicates that many of the reported first hyperpolarizabilities for dipolar molecules from EFISH experiments are most probably underestimated because the Onsager/Lorentz approach, commonly used in extracting the molecular first hyperpolarizability, neglects the effects of the shapes of dipolar chromophore molecules on the local field factors.


Directed evolution of G-protein-coupled receptors for high functional expression and detergent stability.
G-protein-coupled receptors (GPCRs) are cell-surface receptors exhibiting a key role in cellular signal transduction processes, thus making them pharmacologically highly relevant target proteins. However, the molecular mechanisms driving receptor activation by ligand binding and signal transduction are poorly understood, since as integral membrane proteins, most GPCRs are very challenging for functional and structural studies. The biophysical properties of natural GPCRs, usually required by the cell in only low amounts, support their functionality in the lipid bilayer but are insufficient for high-level recombinant overexpression and stability in detergent solution. Current structural information about GPCRs is thus limited to a subset of GPCRs with either intrinsically favorable or properly improved biophysical behavior. Recently, directed protein evolution techniques for functional expression and detergent stability have been developed to increase the accessibility of GPCRs for functional and structural studies. Directed evolution does not rely on any preconceived notion of what might be limiting biophysical properties. By random mutagenesis combined with a high-throughput screening and selection system, directed protein evolution has the power to efficiently isolate rare phenotypes and thus contribute to the elucidation of the stability-determining factors, in addition to solving the practical problem of creating stable GPCRs. In the current chapter, protocols for generation of genetic diversity within GPCRs and selection are provided and discussed.


Differential DNA methylation patterns in human Schlemm's canal endothelial cells with glaucoma.
Schlemm's canal (SC) endothelial cells derived from donors with or without glaucoma showed different mechanical properties and gene expression. As an important contributor to the regulation of intraocular pressure (IOP) and pathogenesis of primary open-angle glaucoma (POAG), the heritable key epigenetic changes, methylation may play an important role in the physiologic function of SC cells. This study aims to identify differentially methylated CpG sites (DMSs) in primary cultures of human SC cells with or without glaucoma. We examined the methylation pattern of seven strains of primary human cells (two glaucoma and five normal SC cell samples), which were isolated and characterized using established protocols. DNA methylation was profiled using Illumina Human Methylation 450 BeadChip. Raw data were extracted and exported using Illumina GenomeStudio software. After quantile normalization, DNA methylation data were analyzed using R package RnBeads in Bioconductor. DMSs were filtered with p ≤ 1E-5, methylation change ≥ 0.1, and false discovery rate ≤ 0.05. The closest genes and the location of each CpG site were annotated using R package FDb.InfiniumMethylation.hg19. Gene Ontology and pathway analysis was performed using WebGestalt. Selected DMSs were validated using the Zymo qMethyl kit. We used five non-glaucoma and two glaucomatous SC cell samples to profile genome-wide DNA methylation using Illumina Infinium Methylation BeadChips. Principle component analysis showed the separation between the glaucoma and control samples. After quality control and differential analysis, we identified 298 highly significant DMSs (p ≤ 1E-5). Among them, 221 DMSs were within 1 kb of a nearby gene. Gene Ontology analysis demonstrated significant enrichment in positive regulation of cell migration, negative regulation of endothelial cell proliferation, and stress fiber and actin filament bundles. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed enrichment in cell adhesion and gap junctions. Several glaucoma-related genes were identified, including TGFBR3, THBS1, PITX2, DAXX, TBX3, TNXB, ANGPT1, and PLEKHA7. We also examined differentially methylated regions (DMRs) near these CpG sites and identified significant DMRs in TBX3, TNXB1, DAXX, and PITX2. This study represents the first genome-wide DNA methylation profiling in cultured human primary SC cells. The DMSs were enriched in the pathways related to outflow resistance. Several DMRs were validated in glaucoma-associated genes, further suggesting the role of DNA methylation in glaucoma development. This study could provide comprehensive understanding of DNA methylation in glaucoma and its effect on aqueous humor outflow.


Metabolic changes following eccentric exercise in trained and untrained men.
The effects of one 45-min bout of high-intensity eccentric exercise (250 W) were studied in four male runners and five untrained men. Plasma creatine kinase (CK) activity in these runners was higher (P less than 0.001) than in the untrained men before exercise and peaked at 207 IU/ml 1 day after exercise, whereas in untrained men the maximum was 2,143 IU/ml 5 days after exercise. Plasma interleukin-1 (IL-1) in the trained men was also higher (P less than 0.001) than in the untrained men before exercise but did not significantly increase after exercise. In the untrained men, IL-1 was significantly elevated 3 h after exercise (P less than 0.001). In the untrained group only, 24-h urines were collected before and after exercise while the men consumed a meat-free diet. Urinary 3-methylhistidine/creatinine in the untrained group rose significantly from 127 mumol/g before exercise to 180 mumol/g 10 days after exercise. The results suggest that in untrained men eccentric exercise leads to a metabolic response indicative of delayed muscle damage. Regularly performed long distance running was associated with chronically elevated plasma IL-1 levels and serum CK activities without acute increases after an eccentric exercise bout.


An Entropy Approach to Disclosure Risk Assessment: Lessons from Real Applications and Simulated Domains.
We live in an increasingly mobile world, which leads to the duplication of information across domains. Though organizations attempt to obscure the identities of their constituents when sharing information for worthwhile purposes, such as basic research, the uncoordinated nature of such environment can lead to privacy vulnerabilities. For instance, disparate healthcare providers can collect information on the same patient. Federal policy requires that such providers share "de-identified" sensitive data, such as biomedical (e.g., clinical and genomic) records. But at the same time, such providers can share identified information, devoid of sensitive biomedical data, for administrative functions. On a provider-by-provider basis, the biomedical and identified records appear unrelated, however, links can be established when multiple providers' databases are studied jointly. The problem, known as trail disclosure, is a generalized phenomenon and occurs because an individual's location access pattern can be matched across the shared databases. Due to technical and legal constraints, it is often difficult to coordinate between providers and thus it is critical to assess the disclosure risk in distributed environments, so that we can develop techniques to mitigate such risks. Research on privacy protection has so far focused on developing technologies to suppress or encrypt identifiers associated with sensitive information. There is growing body of work on the formal assessment of the disclosure risk of database entries in publicly shared databases, but a less attention has been paid to the distributed setting. In this research, we review the trail disclosure problem in several domains with known vulnerabilities and show that disclosure risk is influenced by the distribution of how people visit service providers. Based on empirical evidence, we propose an entropy metric for assessing such risk in shared databases prior to their release. This metric assesses risk by leveraging the statistical characteristics of a visit distribution, as opposed to person-level data. It is computationally efficient and superior to existing risk assessment methods, which rely on ad hoc assessment that are often computationally expensive and unreliable. We evaluate our approach on a range of location access patterns in simulated environments. Our results demonstrate the approach is effective at estimating trail disclosure risks and the amount of self-information contained in a distributed system is one of the main driving factors.


Long-term follow-up study of the Stretta procedure for the treatment of gastroesophageal reflux disease.
The endoscopic delivery of temperature-controlled radiofrequency energy to the gastroesophageal junction (Stretta procedure) recently has been shown effective for patients with gastroesophageal reflux disease (GERD). However, its effectiveness has been assessed mainly over short periods (6-12 months). This study aimed to evaluate long-term results of the Stretta procedure. All patients undergoing the Stretta procedure since August 2000 were prospectively evaluated under an institutional review board-approved protocol. All patients with a follow-up period longer than 18 months were recruited for a 24-h pH study and mailed a follow-up survey, which included the following: Short Form 12 (SF-12) health status questionnaire, GERD-specific quality-of-life questionnaire (QOLRAD), and queries regarding long-term satisfaction and medication use. The Stretta procedure was performed on 82 patients, and 41 patients with a follow-up period longer than 18 months qualified for the study. Follow-up surveys were completed by 36 patients (88%) during a mean follow-up period of 27.1 +/- 3.7 months. Of these 36 patients, 30 (83%) were highly satisfied with the procedure and would have it performed again. More than half of the Fifty Stretta patients (56%) had completely discontinued their use of proton pump inhibitors (PPIs), and an additional 31% had reduced their dose significantly. The mean PPI equivalent doses were 37.8 +/- 22.2 mg/day before the Stretta procedure and 11.6 +/- 14.6 mg/day at 27-month follow-up assessment (p = 0.001). According to the patient outcomes for daily PPI use (yes/no), the patients were divided into two groups: responders (n = 20) and nonresponders (n = 16). The responder group scored higher in QOLRAD score (p = 0.0001), SF-12 physical score (p = 0.038), and SF-12 mental score (p = 0.003). In the 24-hour pH study, the responder group demonstrated a significant decrease in distal esophageal acid exposure time (6.4% +/- 1.5% to 3.1% +/- 1.4%; p = 0.0001). The Stretta procedure results in a statistical significant long-term decrease in GERD symptoms and PPI use. The treatment effect is durable beyond 2 years, and 56% of patients had discontinued their user of all antisecretory drugs.


The potential of sedimentary ancient DNA for reconstructing past sea ice evolution.
Sea ice is a crucial component of the Arctic climate system, yet the tools to document the evolution of sea ice conditions on historical and geological time scales are few and have limitations. Such records are essential for documenting and understanding the natural variations in Arctic sea ice extent. Here we explore sedimentary ancient DNA (aDNA), as a novel tool that unlocks and exploits the genetic (eukaryote) biodiversity preserved in marine sediments specifically for past sea ice reconstructions. Although use of sedimentary aDNA in paleoceanographic and paleoclimatic studies is still in its infancy, we use here metabarcoding and single-species quantitative DNA detection methods to document the sea ice conditions in a Greenland Sea marine sediment core. Metabarcoding has allowed identifying biodiversity changes in the geological record back to almost ~100,000 years ago that were related to changing sea ice conditions. Detailed bioinformatic analyses on the metabarcoding data revealed several sea-ice-associated taxa, most of which previously unknown from the fossil record. Finally, we quantitatively traced one known sea ice dinoflagellate in the sediment core. We show that aDNA can be recovered from deep-ocean sediments with generally oxic bottom waters and that past sea ice conditions can be documented beyond instrumental time scales. Our results corroborate sea ice reconstructions made by traditional tools, and thus demonstrate the potential of sedimentary aDNA, focusing primarily on microbial eukaryotes, as a new tool to better understand sea ice evolution in the climate system.


Older patients referred to a consultation-liaison psychiatry clinic.
Little is known about the psychiatric disorders which are associated with somatic presentations of psychological distress in older people. A study of patients aged 65 years and over referred to an adult consultation-liaison psychiatry clinic in a general hospital. Of 900 patients referred over a 7-year period, 45 (5%) were aged 65 years and over. The most frequent ICD-10 diagnostic category was somatoform disorder (N=30) followed by depressive disorder (N=6). The age of onset of the physical symptoms was significantly earlier in those with somatoform disorders (mean 49 years; SD 3.1 years) compared with patients with depressive disorders (mean 74 years; SD 3.1 years) (p<0.05). All diagnoses were equally associated with moderate functional impairment. Medically unexplained physical symptoms may occur as part of a range of psychiatric disorders in older people and diagnostic groups are distinct in a number of ways. The usefulness of the ICD-10 classification of disorders in relation to these patients is considered. Implications for the delivery of old age psychiatry services are discussed.


A Longitudinal Analysis of Nurse Suicide in the United States (2005-2016) With Recommendations for Action.
Previous studies have demonstrated nurses are at risk of suicide. This is the first national longitudinal study of U.S. nurse suicide. To identify the longitudinal incidence, method, and risks of nurse suicide in the United States. 2005 to 2016 Centers for Disease Control and Prevention National Violent Death Reporting System retrospective analysis of suicide incident rate ratios (IRR). A total of 1,824 nurse and 152,495 non-nurse suicides were evaluated. Nurses were at greater risk of suicide than the general population (female IRR 1.395, 95% confidence intervals [CI] 1.323, 1.470, p < .001; male IRR 1.205, 95% CI 1.083, 1.338, p < .001). Female nurses who completed suicide did so most frequently by pharmacologic poisoning (n = 399, 27.2% vs. n = 8,843, 26.9%), whereby male nurses and the general public used firearms (n = 148, 41.7% vs. n = 57,887, 48.4%). Job problems were more likely in nurses (female odds ratio [OR] 1.989, 95% CI 1.695, 2.325, p < .001; male OR 1.814, 95% CI 1.380, 2.359, p < .001), as well as mental health history (female OR 1.126, 95% CI 1.013, 1.253, p < .027; male OR 1.302, 95% CI 1.048, 1.614, p = .016) and leaving a suicide note (female OR 1.221, 95% CI 1.096, 1.360, p < .001; male OR 1.756 [1.412, 2.181], p < .001). The increased risk of suicide in nurses is congruent with previous reports. The consistency in results increases confidence that findings are generalizable and warrant action. The use of pharmacologic poisoning as a method of suicide, most often by opioids and benzodiazepines, indicates a need for improved identification and treatment of nurses with substance use. Workplace wellness programs need to focus on reducing workplace stressors. Further research is indicated to determine best prevention methods. Policy indications include the need to accurately track gender in nursing, enhance substance use disorder programs, and mandate suicide prevention activities.


HOXB13-to-IL17BR expression ratio is related with tumor aggressiveness and response to tamoxifen of recurrent breast cancer: a retrospective study.
A HOXB13-to-IL17BR expression ratio was previously identified to predict clinical outcome of breast cancer patients treated with adjuvant tamoxifen. However, this ratio may predict a tumor's response to tamoxifen, its intrinsic aggressiveness, or both. We have measured the HOXB13 and IL17BR expression levels by real-time polymerase chain reaction in 1,252 primary breast tumor specimens. Expression levels were normalized to housekeeper gene levels and related to clinicopathologic factors for all patients. The primary objective of this study was to determine the relationship of a HOXB13-to-IL17BR ratio with tumor aggressiveness and/or with response to tamoxifen therapy in estrogen receptor (ER) -positive disease. We selected ER-positive tumors, and clinical end points for the HOXB13-to-IL17BR ratio were disease-free survival (DFS) in patients with primary breast cancer (N = 619) and progression-free survival (PFS) in patients with recurrent breast cancer treated with first-line tamoxifen monotherapy (N = 193). The odds ratio (OR) and hazard ratio (HR) and their 95% CI were calculated, and all P values were two-sided. The HOXB13-to-IL17BR ratio was significantly associated with DFS and PFS. In multivariate analysis, HOXB13-to-IL17BR ratio expression levels were associated with a shorter DFS for node-negative patients only. Corrected for traditional predictive factors, the dichotomized HOXB13-to-IL17BR ratio was the strongest predictor in multivariate analysis for a poor response to tamoxifen therapy (OR = 0.16; 95% CI, 0.06 to 0.45; P < .001) and a shorter PFS (HR = 2.97; 95% CI, 1.82 to 4.86; P < .001). High HOXB13-to-IL17BR ratio expression levels associate with both tumor aggressiveness and tamoxifen therapy failure.


Expression of trypanotolerance in N'Dama x Boran crosses under field challenge in relation to N'Dama genome content.
Animal trypanosomosis in sub-Saharan Africa is a major obstacle to livestock based agriculture. Control relies on drugs with increasing incidence of multiple-drug resistance. A previous mapping experiment in an F2 population derived from the indigenous trypanotolerant N'Dama cattle crossed to susceptible (Kenya)-Boran cattle under controlled challenge, uncovered a number of trypanotolerance QTL (T-QTL). The present study was to determine expression of N'Dama trypanotolerance in a backcross to the Boran under conditions of field challenge, and whether chromosomal regions associated with trypanotolerance in the F2 experiment showed similar effects in the BC population. 192 backcross animals to the Boran were produced in six batches from June 2001 to December 2006. At one year of age animals were moved to the field and exposed to natural challenge over about one year in Southwest Kenya (Narok). The animals were individually recorded weekly for body weight, packed cell volume, parasitaemia score, and drug treatments, and were genotyped using 35 microsatellite markers spanning 5 chromosomes found in the F2 study to harbour T-QTL. The F1 were most trypanotolerant, Boran least, and BC intermediate. Females showed distinctly higher trypanotolerance than males. There was a positive correlation in the BC population between trypanotolerance and number of N'Dama origin marker alleles. QTL mapping revealed T-QTL distributed among all five targeted chromosomes, corresponding in part to the results obtained in the F2 experiment. N'Dama origin trypanotolerance is expressed in a BC population under field conditions in proportion to N'Dama origin marker alleles. Consequently, marker assisted selection in such populations may be a means of increasing trypanotolerance, while retaining the desirable productive qualities of the recurrent parent.


Porous clinoptilolite-nano biphasic calcium phosphate scaffolds loaded with human dental pulp stem cells for load bearing orthopedic applications.
Clinoptilolite (Cpt)-nanohydroxyapatite (HA) (Cpt-HA) scaffolds were fabricated as a potential material for loadbearing orthopaedic applications. Cpt-HA materials were successfully synthesized by using microwave assisted reflux method followed by the fabrication of three-dimensional (3D) porous scaffold via thermal decomposition process using polyethylene glycol (PEG)/ polyvinyl alcohol (PVA) as porogens. The scaffold materials were characterized using x-ray diffraction, Fourier transform Infra-red, Scanning electron microscopy and Energy dispersive spectroscopy techniques. Incorporation of Cpt in HA scaffold significantly increased the compressive strength and surface hardness while scaffolds retained an interconnected porous structure with 64% porosity. Human dental pulp stem cells (DPSCs) were isolated from the third molar and used as pluripotent-like cell model to evaluate the biological properties of Cpt-HA scaffolds. Highest cellular attachment and proliferation were observed for DPSCs seeded on 2.0 g Cpt-HA scaffolds compare to pure HA. Similarly, significantly higher ALP activity of cells was observed on Cpt-HA scaffolds compared to pure HA. The enhanced proliferation and osteogenic response of the DPSCs cultured on Cpt-HA scaffolds suggest that the fabricated scaffolds can be used in bone tissue engineering. In this work, we have successfully shown that the interconnected porous Cpt-HA scaffolds have superior mechanical biological properties compared to pure HA scaffold.


Chromosome aberrations in workers with exposure to α-particle radiation from internal deposits of plutonium: expectations from in vitro studies and comparisons with workers with predominantly external γ-radiation exposure.
mFISH analysis of chromosome aberration profiles of 47 and 144 h lymphocyte cultures following exposure to 193 mGy α-particle radiation confirmed that the frequency of stable aberrant cells and stable cells carrying translocations remains constant through repeated cell divisions. Age-specific rates and in vitro dose-response curves were used to derive expected translocation yields in nine workers from the Mayak nuclear facility in Russia. Five had external exposure to γ-radiation, two of whom also had exposure to neutrons, and four had external exposure to γ-radiation and internal exposure to α-particle radiation from incorporated plutonium. Doubts over the appropriateness of the dose response used to estimate translocations from the neutron component made interpretation difficult in two of the workers with external exposure, but the other three had translocation yields broadly in line with expectations. Three of the four plutonium workers had translocation yields in line with expectations, thus supporting the application of the recently derived in vitro α-particle dose response for translocations in stable cells. Overall this report demonstrates that with adequate reference in vitro dose-response curves, translocation yield has the potential to be a useful tool in the validation of red bone marrow doses resulting from mixed exposure to external and internal radiation.


Service-based analysis of biological pathways.
Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper.


Restless legs syndrome: epidemiological and clinicogenetic study in a South Tyrolean population isolate.
Genetic contributions to restless legs syndrome (RLS) have been consistently recognized from population and family studies. To determine the clinical and genetic features of RLS in a population isolate and explore linkage to three previously described susceptibility loci on chromosomes 12q, 14q, and 9p, respectively, an isolated population in the South Tyrolean Alps was identified and 530 adults participated in the study. Using a two-step strategy, 47 patients with idiopathic RLS were ascertained. The prevalence in the population was 8.9%. Twenty-eight patients (59.6%) had at least one affected first-degree relative and were classified as hereditary cases. In a single extended pedigree, linkage to known RLS loci was investigated specifying autosomal dominant and recessive models; parametric and nonparametric multipoint linkage scores were computed. None of the calculated linkage scores was suggestive of linkage between RLS and any of the three investigated loci. This study was conducted in a population isolate providing for a homogeneous genetic and environmental background. The absence of a suggestive linkage signal at the three known RLS susceptibility loci is indicative of further locus heterogeneity of this frequent disorder and encourages further studies to unveil the genetic causes of RLS.


Weeds in Greenhouses and Tobacco Fields Are Differentially Infected by Tomato spotted wilt virus and Infested by Its Vector Species.
A survey was conducted in the Macedonia region of Greece to determine the reservoir hosts of Tomato spotted wilt virus (TSWV) in three tobacco fields and in a greenhouse complex in which lettuce and the ornamentals chrysanthemum, gerbera, aster, and anemone were grown. Assays for TSWV infection were made by enzyme-linked immunosorbent assay on 6,172 plant samples, 3,909 from tobacco fields and 2,263 from the greenhouse complex, comprising plants of 208 species in 137 genera of 42 families. Plants of 86 species out of 63 genera of 27 families were infected of which 39 species are newly reported hosts of TSWV. An infection index was developed to evaluate the relative potential of each weed species as a virus source in both systems. Seventeen species in the tobacco fields and nine in the greenhouses had an infection index higher than one. Most species with infected plants were found in the Compositae family. Plants of some species occurring both in tobacco fields and in greenhouses were infected at only one of these sites. Frankliniella occidentalis was the common thrips species on weeds and crops in the greenhouses, while Thrips tabaci was the only vector on tobacco plants and weeds in the tobacco fields. This observation strongly suggests that the occurrence of species with infected plants and their number have to be attributed to the vector species prevailing in the greenhouse complex or tobacco fields, supporting the conclusion that TSWV is spread in two different epidemiological processes in Greece.


Glycopeptides as Targets for Dendritic Cells: Exploring MUC1 Glycopeptides Binding Profile toward Macrophage Galactose-Type Lectin (MGL) Orthologs.
The macrophage galactose-type lectin (MGL) recognizes glycan moieties exposed by pathogens and malignant cells. Particularly, mucin-1 (MUC1) glycoprotein presents an altered glycosylation in several cancers. To estimate the ability of distinct MGL orthologs to recognize aberrant glycan cores in mucins, we applied evanescent-field detection to a versatile MUC1-like glycopeptide microarray platform. Here, as binding was sequence-dependent, we demonstrated that not only sugars but also peptide region impact the recognition of murine MGL1 (mMGL1). In addition, we observed for all three MGL orthologs that divalent glycan presentation increased the binding. To assess the utility of the glycopeptide binders of the MGL orthologs for MGL targeting, we performed uptake assays with fluorescein-MUC1 using murine dendritic cells. A diglycosylated MUC1 peptide was preferentially internalized in an MGL-dependent fashion, thus showing the utility for divalent MGL targeting. These findings may be relevant to a rational design of antitumor vaccines targeting dendritic cells via MGL.


Comparison of high frequency chest compression and conventional chest physiotherapy in hospitalized patients with cystic fibrosis.
Clearance of bronchial secretions is essential in the management of cystic fibrosis (CF) patients admitted for acute pulmonary exacerbation. Conventional physiotherapy (CPT) is labor-intensive, time-consuming, expensive, and may not be available as frequently as desired during hospitalization. High frequency chest compression (HFCC), which uses an inflatable vest linked to an air-pulse delivery system, may offer an attractive alternative. To study this, we prospectively studied 50 CF patients admitted for acute pulmonary exacerbation who were randomly allocated to receive either HFCC or CPT three times a day. On admission, clinical status and pulmonary function tests (PFT) in the HFCC group were not significantly different from those measured in the CPT group. Significant improvements in clinical status and PFT were observed after 7 and 14 d of treatment, and were similar in the two study groups, leading to patient discharge after similar periods of hospitalization. We conclude that HFCC and CPT are equally safe and effective when used during acute pulmonary exacerbations in CF patients. We speculate that HFCC may provide an adequate alternative in management of CF patients in a hospital setting.


Green tea or rosemary extract added to foods reduces nonheme-iron absorption.
Phenolic compounds act as food antioxidants. One of the postulated mechanisms of action is chelation of prooxidant metals, such as iron. Although the antioxidative effect is desirable, this mechanism may impair the utilization of dietary iron. We sought to determine the effect of phenolic-rich extracts obtained from green tea or rosemary on nonheme-iron absorption. Young women aged 19-39 y consumed test meals on 4 separate occasions. The meals were identical except for the absence (meal A) or presence (meal B) of a phenolic-rich extract from green tea (study 1; n = 10) or rosemary (study 2; n = 14). The extracts (0.1 mmol) were added to the meat component of the test meals. The meals were extrinsically labeled with either 55Fe or 59Fe and were consumed on 4 consecutive days in the order ABBA or BAAB. Iron absorption was determined by measuring whole-body retention of 59Fe and the ratio of 55Fe to 59Fe activity in blood samples. The presence of the phenolic-rich extracts resulted in decreased nonheme-iron absorption. Mean (+/-SD) iron absorption decreased from 12.1 +/- 4.5% to 8.9 +/- 5.2% (P < 0.01) in the presence of green tea extract and from 7.5 +/- 4.0% to 6.4 +/- 4.7% (P < 0.05) in the presence of rosemary extract. Phenolic-rich extracts used as antioxidants in foods reduce the utilization of dietary iron.


Visual determinants of a cross-modal illusion.
Contrary to the predictions of established theory, Schutz and Lipscomb (2007) have shown that visual information can influence the perceived duration of concurrent sounds. In the present study, we deconstruct the visual component of their illusion, showing that (1) cross-modal influence depends on visible cues signaling an impact event (namely, a sudden change of direction concurrent with tone onset) and (2) the illusion is controlled primarily by the duration of post-impact motion. Other aspects of the post-impact motion--distance traveled, velocity, acceleration, and the rate of its change (i.e., its derivative, jerk)--play a minor role, if any. Together, these results demonstrate that visual event duration can influence the perception of auditory event duration, but only when stimulus cues are sufficient to give rise to the perception of a causal cross-modal relationship. This refined understanding of the illusion's visual aspects is helpful in comprehending why it contrasts so markedly with previous research on cross-modal integration, demonstrating that vision does not appreciably influence auditory judgments of event duration (Walker & Scott, 1981).


A Multi-Functional CMOS Biosensor Array with On-Chip DEP-Assisted Sensing for Rapid Low-Concentration Analyte Detection and Close-Loop Particle Manipulation with No External Electrodes.
This article presents a fully-integrated dielectrophoresis (DEP)-assisted multi-functional CMOS biosensor array chip with 4096 working electrodes (WEs), 12288 photodiodes (PDs), reference electrodes (REs), and counter electrodes (CEs), while each WE and photodiode can be reconfigured to support on-chip DEP actuation, electrochemical potentiostat, optical shadow imaging, and complex impedance sensing. The proposed CMOS biosensor is an example of an actuation-assisted label-free biosensor for the rapid sensing of low-concentration analytes. The DEP actuator of the proposed CMOS biosensor does not require any external electrode. Instead, on-chip WE pairs can be re-used for DEP actuation to simplify the sensor array design. The CMOS biosensor is implemented in a standard 130-nm BiCMOS process. Theoretical analyses and finite element method (FEM) simulations of the on-chip DEP operations are conducted as proof of concept. Biological assay measurements (DEP actuation/electrochemical potentiostat/impedance sensing) with E. coli bacteria and microbeads (optical shadow imaging) demonstrate rapid detection of low-concentration analytes and simultaneous manipulation and detection of large particles. The on-chip DEP operations draw the analytes closer to the sensor electrode surface, which overcomes the diffusion limit and accelerates low-concentration analyte sensing. Moreover, the DEP-based movement of large particles can be readily detected by on-chip photodiode arrays to achieve close-loop manipulation and sensing of particles and droplets. These show the unique advantages of the DEP-assisted multi-functional biosensor.


CD3 monoclonal antibodies: a first step towards operational immune tolerance in the clinic.
Type 1 diabetes (T1D) is a prototypic organ-specific autoimmune disease resulting from the selective destruction of insulin-secreting β-cells within the pancreatic islets of Langerhans. It is caused by an immune-mediated inflammation, involving autoreactive CD4⁺ and CD8⁺ T lymphocytes that infiltrate the islets and initiate insulitis. The use of exogenous insulin is the current standard treatment. However, in spite of significant advances, this therapy is still associated with major constraints, including risk of hypoglycemia and severe degenerative complications. As T1D mainly affects children and young adults, any candidate immune therapy must be safe, and it must avoid a sustained depression of immune responses with all its attendant problems of recurrent infection and drug toxicity. In this context, inducing or restoring immune tolerance to target autoantigens would be the ideal approach. We refer to immune tolerance here as the selective damping of the damaging autoimmune response following a short treatment, while keeping intact the capacity of the host to respond normally to exogenous antigens. The therapeutic approach we discuss in this article originates from attempts to induce tolerance both to soluble antigens and tissue antigens (i.e. alloantigens and autoantigens) by using biological agents that selectively interfere with lymphocyte activation, namely polyclonal and monoclonal anti-T cell antibodies. The challenged dogma was that, in an adult-primed immune system, it was not possible to restore self-tolerance therapeutically without the use of exogenous autoantigen administration. The reality has been that, in diabetes, endogenous host autoantigen can fulfill this role because a significant amount of functioning β-cells remains, even at the time of established hyperglycemia. Experimental results obtained in the 1990s showed that a short-term CD3 antibody treatment in recently diagnosed diabetic non-obese diabetic (NOD) mice induced permanent remission of the disease by restoring self-tolerance. Based on these findings, phase I, II, and III trials were conducted using two distinct humanized Fc-mutated antibodies to human CD3, namely ChAglyCD3 (otelixizumab) and OKT3γ1 Ala-Ala (teplizumab). Overall, when dosing was adequate, the results demonstrated that CD3 antibodies preserved β-cell function very efficiently, maintaining significantly high levels of endogenous insulin secretion in treated patients for up to 24 months after treatment. These data provided the first proof of concept for a long-term therapeutic effect in T1D following a short course administration of a therapeutic agent. Our aim is to review these data and to discuss them in the context of the pitfalls linked to pharmaceutical development, especially in the context of pediatric patients, as in autoimmune diabetes.


Using fatty-acid profile analysis as an ecologic indicator in the management of tourist impacts on marine wildlife: a case of stingray-feeding in the Caribbean.
Feeding marine wildlife as a tourism experience has become a popular means by which to attract both people and wildlife, although management efforts are still in their infancy. "Stingray City Sandbar" in the Cayman Islands, where visitors can hand feed free-ranging Southern Stingrays (Dasyatis americana), is a world-famous attraction currently undergoing visitor and wildlife management. One plan is to decrease the amount of nonnatural food provided by tourists with the intention of decreasing stingray habituation to the artificial food source and promoting stingray health. However, the effectiveness of this action is uncertain given that neither the extent of squid composition in the stingray diet nor the degree of nutrient similarity between the fed and natural diets is unknown. We used fatty acid (FA) profile analysis to address these questions by assessing the serum nonesterified FA composition of fed and unfed stingrays around the island and compared them with FA profiles of (1) the provisioned food source (squid) and (2) other warm- and cold-water elasmobranchs (sharks and rays). Our results indicated that fed stingrays were distinct. The FA profiles of the fed stingray population were expressly different from those of the unfed populations and showed a remarkable similarity to the FA composition of squid, suggesting that squid is the main food source. The tropical fed stingrays also exhibited essential FA ratios, specific to both species and habitat, comparable with those of elasmobranchs and squid from cold-water environs, implying that the provisioned food does not provide a similar nutritional lipid composition to that eaten in the wild. Our results suggest that FA profiles are a valuable indicator for the management and monitoring of fed Southern Stingrays because they can be used to assess differences in diet composition and provide an index of nutritional similarity. Our findings are currently being used by Caymanian stakeholders in designing practical management actions for their wildlife attraction.


Incorporation of strontium and europium in crystals of α-calcium isosaccharinate.
The final repository for short-lived, low and intermediate level radioactive waste in Sweden is built to act as a passive repository. Already within a few years after closure water will penetrate the repository and conditions of high alkalinity (pH 10.5-13.5) and low temperature (< 7 °C) will prevail. The mobility of radionuclides in the repository is dependent on the radionuclides distribution between solid and liquid phases. In the present work the incorporation of strontium (II) and europium (III) in α-calcium isosaccharinate (ISA) under alkaline conditions (pH ∼10) at 5 °C and 50 °C have been studied. The results show that strontium and europium are incorporated into α-Ca(ISA)2 when crystallized both at 5 °C and 50 °C. Europium is incorporated to a greater extent than strontium. The highest incorporation of europium and strontium at 5 °C rendered the phase compositions Ca0.986Eu0.014(ISA)2 (2.4% of Eu(ISA)3 by mass) and Ca0.98Sr0.02(ISA)2 (2.2% of Sr(ISA)2 by mass). XPS spectra show that both trivalent and divalent Eu coexist in the Eu incorporated samples. Strontium ions were found to retard the elongated growth of the Ca(ISA)2 crystals. The incorporation of Sr2+ and Eu3+ into the solid phase of Ca(ISA)2 is expected to contribute to a decreased mobility of these ions in the repository.


Phytochemicals for Improving Aspects of Cognitive Function and Psychological State Potentially Relevant to Sports Performance.
Subjective alertness and optimal cognitive function, including in terms of attention, spatial/working memory and executive function, are intrinsic to peak performance in many sports. Consumption of a number of plant-derived 'secondary metabolite' phytochemicals can modulate these psychological parameters, although there is a paucity of evidence collected in a sporting context. The structural groups into which these phytochemicals fall-phenolics, terpenes and alkaloids-vary in terms of the ecological roles they play for the plant, their toxicity and the extent to which they exert direct effects on brain function. The phenolics, including polyphenols, play protective roles in the plant, and represent a natural, benign component of the human diet. Increased consumption has been shown to improve cardiovascular function and is associated with long-term brain health. However, whilst short-term supplementation with polyphenols has been shown to consistently modulate cerebral blood-flow parameters, evidence of direct effects on cognitive function and alertness/arousal is currently comparatively weak. Terpenes play both attractant and deterrent roles in the plant, and typically occur less frequently in the diet. Single doses of volatile monoterpenes derived from edible herbs such as sage (Salvia officinalis/lavandulaefolia) and peppermint (Mentha piperita), diterpene-rich Ginkgo biloba extracts and triterpene-containing extracts from plants such as ginseng (Panax ginseng/quinquefolius) and Bacopa monnieri have all been shown to enhance relevant aspects of cognitive function and alertness. The alkaloids play toxic defensive roles in the plant, including via interference with herbivore brain function. Whilst most alkaloids are inappropriate in a sporting context due to toxicity and legal status, evidence suggests that single doses of nicotine and caffeine may be able to enhance relevant aspects of cognitive function and/or alertness. However, their benefits may be confounded by habituation and withdrawal effects in the longer term. The efficacy of volatile terpenes, triterpene-rich extracts and products combining low doses of caffeine with other phytochemicals deserves more research attention.


Extraction of respiratory signals from the electrocardiogram and photoplethysmogram: technical and physiological determinants.
Breathing rate (BR) can be estimated by extracting respiratory signals from the electrocardiogram (ECG) or photoplethysmogram (PPG). The extracted respiratory signals may be influenced by several technical and physiological factors. In this study, our aim was to determine how technical and physiological factors influence the quality of respiratory signals. Using a variety of techniques 15 respiratory signals were extracted from the ECG, and 11 from PPG signals collected from 57 healthy subjects. The quality of each respiratory signal was assessed by calculating its correlation with a reference oral-nasal pressure respiratory signal using Pearson's correlation coefficient. Relevant results informing device design and clinical application were obtained. The results informing device design were: (i) seven out of 11 respiratory signals were of higher quality when extracted from finger PPG compared to ear PPG; (ii) laboratory equipment did not provide higher quality of respiratory signals than a clinical monitor; (iii) the ECG provided higher quality respiratory signals than the PPG; (iv) during downsampling of the ECG and PPG significant reductions in quality were first observed at sampling frequencies of <250 Hz and <16 Hz respectively. The results informing clinical application were: (i) frequency modulation-based respiratory signals were generally of lower quality in elderly subjects compared to young subjects; (ii) the qualities of 23 out of 26 respiratory signals were reduced at elevated BRs; (iii) there were no differences associated with gender. Recommendations based on the results are provided regarding device designs for BR estimation, and clinical applications. The dataset and code used in this study are publicly available.


Moderate-resolution imaging spectroradiometer ocean color polarization correction.
The polarization correction for the Moderate-Resolution Imaging Spectroradiometer (MODIS) instruments on the Terra and Aqua satellites is described. The focus is on the prelaunch polarization characterization and on the derivation of polarization correction coefficients for the processing of ocean color data. The effect of the polarization correction is demonstrated. The radiances at the top of the atmosphere need to be corrected by as much as 3.2% in the 412 nm band. The effect on the water-leaving radiances can exceed 50%. The polarization correction produces good agreement of the MODIS Aqua water-leaving radiance time series with data from another, independent satellite-based ocean color sensor, the Sea-Viewing Wide Field-of-View Sensor (SeaWiFS).


Functional outcome after anal sphincter injury and treatment with mesenchymal stem cells.
This research demonstrates the regenerative effects of mesenchymal stem cells (MSCs) on the injured anal sphincter by comparing anal sphincter pressures following intramuscular and serial intravascular MSC infusion in a rat model of anal sphincter injury. Fifty rats were divided into injury (n = 35) and no injury (NI; n = 15) groups. Each group was further divided into i.m., serial i.v., or no-treatment (n = 5) groups and followed for 5 weeks. The injury consisted of an excision of 25% of the anal sphincter complex. Twenty-four hours after injury, 5 × 10(5) green fluorescent protein-labeled MSCs in 0.2 ml of phosphate-buffered saline (PBS) or PBS alone (sham) were injected into the anal sphincter for i.m. treatment; i.v. and sham i.v. treatments were delivered daily for 6 consecutive days via the tail vein. Anal pressures were recorded before injury and 10 days and 5 weeks after treatment. Ten days after i.m. MSC treatment, resting and peak pressures were significantly increased compared with those in sham i.m. treatment (p < .001). When compared with the NI group, the injury groups had anal pressures that were not significantly different 5 weeks after i.m./i.v. treatment. Both resting and peak pressures were also significantly increased after i.m./i.v. MSC treatment compared with treatment with PBS (p < .001), suggesting recovery. Statistical analysis was done using paired t test with Bonferroni correction. Marked decrease in fibrosis and scar tissue was seen in both MSC-treated groups. Both i.m. and i.v. MSC treatment after injury caused an increase in anal pressures sustained at 5 weeks, although fewer cells were injected i.m. The MSC-treated groups showed less scarring than the PBS-treated groups, with the i.v. infusion group showing the least scarring.


The impact of patient race on clinical decisions related to prescribing HIV pre-exposure prophylaxis (PrEP): assumptions about sexual risk compensation and implications for access.
Antiretroviral pre-exposure prophylaxis (PrEP) has received increasing recognition as a viable prescription-based intervention for people at risk for HIV acquisition. However, little is known about racial biases affecting healthcare providers' willingness to prescribe PrEP. This investigation sought to explore medical students' stereotypes about sexual risk compensation among Black versus White men who have sex with men seeking PrEP, and the impact of such stereotypes on willingness to prescribe PrEP. An online survey presented participants (n = 102) with a clinical vignette of a PrEP-seeking, HIV-negative man with an HIV-positive male partner. Patient race was systematically manipulated. Participants reported predictions about patient sexual risk compensation, willingness to prescribe PrEP, and other clinical judgments. Bootstrapping analyses revealed that the Black patient was rated as more likely than the White patient to engage in increased unprotected sex if prescribed PrEP, which, in turn, was associated with reduced willingness to prescribe PrEP to the patient.


ClusCo: clustering and comparison of protein models.
The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline. Clusco is fast and easy-to-use software for high-throughput comparison of protein models with different similarity measures (cRMSD, dRMSD, GDT_TS, TM-Score, MaxSub, Contact Map Overlap) and clustering of the comparison results with standard methods: K-means Clustering or Hierarchical Agglomerative Clustering. The application was highly optimized and written in C/C++, including the code for parallel execution on CPU and GPU, which resulted in a significant speedup over similar clustering and scoring computation programs.


The winding road to health: A systematic scoping review on the effect of geographical accessibility to health care on infectious diseases in low- and middle-income countries.
Geographical accessibility to healthcare is an important component of infectious disease dynamics. Timely access to health facilities can prevent disease progression and enables disease notification through surveillance systems. The importance of accounting for physical accessibility in response to infectious diseases is increasingly recognized. Yet, there is no comprehensive review of the literature available on infectious diseases in relation to geographical accessibility to care. Therefore, we aimed at evaluating the current state of knowledge on the effect of geographical accessibility to health care on infectious diseases in low- and middle-income countries. A search strategy was developed and conducted on Web of Science and PubMed on 4 March 2019. New publications were checked until May 28, 2020. All publication dates were eligible. Data was charted into a tabular format and descriptive data analyses were carried out to identify geographical regions, infectious diseases, and measures of physical accessibility among other factors. Search queries in PubMed and Web of Science yielded 560 unique publications. After title and abstract screening 99 articles were read in full detail, from which 64 articles were selected, including 10 manually. Results of the included publications could be broadly categorized into three groups: (1) decreased spatial accessibility to health care was associated with a higher infectious disease burden, (2) decreased accessibility was associated to lower disease reporting, minimizing true understanding of disease distribution, and (3) the occurrence of an infectious disease outbreak negatively impacted health care accessibility in affected regions. In the majority of studies, poor geographical accessibility to health care was associated with higher disease incidence, more severe health outcomes, higher mortality, and lower disease reporting. No difference was seen between countries or infectious diseases. Currently, policy-makers and scientists rely on data collected through passive surveillance systems, introducing uncertainty on disease estimates for remote communities. Our results highlight the need for increasing integration of geographical accessibility measures in disease risk modelling, allowing more realistic disease estimates and enhancing our understanding of true disease burden. Additionally, disease risk estimates could be used in turn to optimize the allocation of health services in the prevention and detection of infectious diseases.


Plasma carotenoids and vitamin C concentrations and risk of urothelial cell carcinoma in the European Prospective Investigation into Cancer and Nutrition.
Published associations between dietary carotenoids and vitamin C and bladder cancer risk are inconsistent. Biomarkers may provide more accurate measures of nutrient status. We investigated the association between plasma carotenoids and vitamin C and risk of urothelial cell carcinoma (UCC) in a case-control study nested within the European Prospective Investigation into Cancer and Nutrition. A total of 856 patients with newly diagnosed UCC were matched with 856 cohort members by sex, age at baseline, study center, date and time of blood collection, and fasting status. Plasma carotenoids (α- and β-carotene, β-cryptoxanthin, lycopene, lutein, and zeaxanthin) were measured by using reverse-phase HPLC, and plasma vitamin C was measured by using a colorimetric assay. Incidence rate ratios (IRRs) were estimated by using conditional logistic regression with adjustment for smoking status, duration, and intensity. UCC risk decreased with higher concentrations of the sum of plasma carotenoids (IRR for the highest compared with the lowest quartile: 0.64; 95% CI: 0.44, 0.93; P-trend = 0.04). Plasma β-carotene was inversely associated with aggressive UCC (IRR: 0.51; 95% CI: 0.30, 0.88; P-trend = 0.02). Plasma lutein was inversely associated with risk of nonaggressive UCC (IRR: 0.56; 95% CI: 0.32, 0.98; P-trend = 0.05). No association was observed between plasma vitamin C and risk of UCC. Although residual confounding by smoking or other factors cannot be excluded, higher concentrations of plasma carotenoids may reduce risk of UCC, in particular aggressive UCC. Plasma lutein may reduce risk of nonaggressive UCC.


Observations on the Early Establishment of Foliar Endophytic Fungi in Leaf Discs and Living Leaves of a Model Woody Angiosperm, Populus trichocarpa (Salicaceae).
Fungal endophytes are diverse and widespread symbionts that occur in the living tissues of all lineages of plants without causing evidence of disease. Culture-based and culture-free studies indicate that they often are abundant in the leaves of woody angiosperms, but only a few studies have visualized endophytic fungi in leaf tissues, and the process through which most endophytes colonize leaves has not been studied thoroughly. We inoculated leaf discs and the living leaves of a model woody angiosperm, Populus trichocarpa, which has endophytes that represent three distantly-related genera (Cladosporium, Penicillium, and Trichoderma). We used scanning electron microscopy and light microscopy to evaluate the timeline and processes by which they colonize leaf tissue. Under laboratory conditions with high humidity, conidia germinated on leaf discs to yield hyphae that grew epiphytically and incidentally entered stomata, but did not grow in a directed fashion toward stomatal openings. No cuticular penetration was observed. The endophytes readily colonized the interiors of leaf discs that were detached from living leaves, and could be visualized within discs with light microscopy. Although they were difficult to visualize within the interior of living leaves following in vivo inoculations, standard methods for isolating foliar endophytes confirmed their presence.


By design: a macrocyclic 3d-4f single-molecule magnet with quantifiable zero-field slow relaxation of magnetization.
Rational modification of the equatorially bound tetranucleating macrocycle in the previously reported SMM complex of the propylene linked macrocycle [Cu(II)3Tb(III)(L(Pr))](NO3)2, to a new butylene linked analogue, is shown to tune the ligand field imposed on the encapsulated Cu(II)3Tb(III) cluster. This results in apical binding of two, rather than one, nitrate ions to the oblate Tb(III) ion, giving enhanced uniaxial anisotropy and SMM properties despite the low symmetry of the Tb(III) site. The resulting complex, [Cu(II)3Tb(III)(L(Bu))(NO3)2(MeOH)(H2O)](NO3)·3H2O, is the first example of a macrocyclic 3d-4f single-molecule magnet that exhibits quantifiable relaxation of magnetization in zero dc field (Δ(eff)/k(B) = 19.5(5) K; τ0 = 3.4 × 10(-7) s). This SMM complex of this new, larger, tetranucleating macrocycle was prepared by the template method from the 3:3:3:1 reaction of 1,4-diformyl-2,3-dihydroxybenzene/diaminobutane/copper(II) acetate/terbium(III) nitrate. Similarly, the analogues, Zn3Tb(L(Bu))(NO3)3·MeOH·H2O·DMF and [Cu3La(L(Bu))(NO3)2(MeOH)(H2O)2](NO3)·H2O·DMF, were prepared in order to facilitate the detailed magnetic analysis. Both copper(II) complexes were also structurally characterized, confirming the expected binding mode: lanthanide(III) ion in the central O6 pocket, and the three copper(II) ions in the outer N2O2 pockets.