Light quality-mediated petiole elongation in Arabidopsis during shade avoidance involves cell wall modification by xyloglucan endotransglucosylase/hydrolases.
Some plants can avoid shaded conditions via rapid shoot elongation, thus growing into better lit areas in a canopy. Cell wall-modifying mechanisms promoting this elongation response, therefore, are important regulatory points during shade avoidance. Two major cell wall-modifying protein families are expansins and xyloglucan endotransglucosylase/hydrolases (XTHs). The role of these proteins during shade avoidance was studied in Arabidopsis (Arabidopsis thaliana). In response to two shade cues, low red to far-red light (implying neighbor proximity) and green shade (mimicking dense canopy conditions), Arabidopsis showed classic shade avoidance features: petiole elongation and leaf hyponasty. Measurement of the apoplastic proton flux in green shade-treated petioles revealed a rapid efflux of protons into the apoplast within minutes, unlike white light controls. This apoplastic acidification probably provides the acidic pH required for the optimal activity of cell wall-modifying proteins like expansins and XTHs. Acid-induced extension, expansin susceptibility, and extractable expansin activity were similar in petioles from white light- and shade-treated plants. XTH activity, however, was high in petioles exposed to shade treatments. Five XTH genes (XTH9, -15, -16, -17, and -19) were positively regulated by low red to far-red light conditions, while the latter four and XTH22 showed a significant up-regulation also in response to green shade. Consistently, knockout mutants for two of these XTH genes also had reduced or absent shade avoidance responses to these light signals. These results point toward the cell wall as a vital regulatory point during shade avoidance.


Report on ISCTM Consensus Meeting on Clinical Assessment of Response to Treatment of Cognitive Impairment in Schizophrenia.
If treatments for cognitive impairment are to be utilized successfully, clinicians must be able to determine whether they are effective and which patients should receive them. In order to develop consensus on these issues, the International Society for CNS Clinical Trials and Methodology (ISCTM) held a meeting of experts on March 20, 2014, in Washington, DC. Consensus was reached on several important issues. Cognitive impairment and functional disability were viewed as equally important treatment targets. The group supported the notion that sufficient data are not available to exclude patients from available treatments on the basis of age, severity of cognitive impairment, severity of positive symptoms, or the potential to benefit functionally from treatment. The group reached consensus that cognitive remediation is likely to provide substantial benefits in combination with procognitive medications, although a substantial minority believed that medications can be administered without nonpharmacological therapy. There was little consensus on the best methods for assessing cognitive change in clinical practice. Some participants supported the view that performance-based measures are essential for measurement of cognitive change; others pointed to their cost and time requirements as evidence of impracticality. Interview-based measures of cognitive and functional change were viewed as more practical, but lacking validity without informant involvement or frequent contact from clinicians. The lack of consensus on assessment methods was viewed as attributable to differences in experience and education among key stakeholders and significant gaps in available empirical data. Research on the reliability, validity, sensitivity, and practicality of competing methods will facilitate consensus.


Modeling resistance to genetic control of insects.
The sterile insect technique is an area-wide pest control method that reduces pest populations by releasing mass-reared sterile insects which compete for mates with wild insects. Modern molecular tools have created possibilities for improving and extending the sterile insect technique. As with any new insect control method, questions arise about potential resistance. Genetic RIDL(®)(1) (Release of Insects carrying a Dominant Lethal) technology is a proposed modification of the technique, releasing insects that are homozygous for a repressible dominant lethal genetic construct rather than being sterilized by irradiation. Hypothetical resistance to the lethal mechanism is a potential threat to RIDL strategies' effectiveness. Using population genetic and population dynamic models, we assess the circumstances under which monogenic biochemically based resistance could have a significant impact on the effectiveness of releases for population control. We assume that released insects would be homozygous susceptible to the lethal genetic construct and therefore releases would have a built-in element of resistance dilution. We find that this effect could prevent or limit the spread of resistance to RIDL constructs; the outcomes are subject to competing selective forces deriving from the fitness properties of resistance and the release ratio. Resistance that is spreading and capable of having a significant detrimental impact on population reduction is identifiable, signaling in advance a need for mitigating action.


Use of marijuana for medical purposes.
Cannabis is the most popular illicit drug on the European market. Over 16 million young Europeans have used it at least once in the last few years. The recent trends in the consumption of marihuana differ between countries. Some countries face an increase in the prevalence of cannabis use, including Poland, where the level cannabis use has been systematically increasing since the 1990's. According to a recent ESPAD study, 19% of Polish adolescents aged 15-16 have used cannabis in the last year. Marihuana is also a leading substance when analyzing the data of seizures and crimes. The recent EMCDDA Annual report on the drug situation in Europe notes the increasing potency in cannabis available on the market. Some countries face an increasing number of emergencies caused by marihuana, which was unlikely to have happened previously. In almost all European countries there is an ongoing discussion about loosening marijuana laws or its complete legalization. There is also ongoing discussion on the use of marihuana in therapy as a medicine. Many scientific studies are being conducted in this field. Some of the results are promising; however, there is no well-designed human trial which would unequivocally confirm that medical cannabis is effective as a medicine, or more effective than other medicines on the market. The problem is that the debate on the medical use of marihuana becomes more ideological and less professional. The medical use of marihuana is strongly supported by organizations lobbying for the legalization of cannabis use. Research on the medical use of cannabis should be continued, as there are some promising results supporting therapy in different medical conditions. However, the use of cannabis as a medicine should be discussed only among professionals. If marihuana is to be used for medical purposes, the fact that it is the most popular illicit drug in Europe is irrelevant.


Reaction dynamics inside superfluid helium nanodroplets: the formation of the Ne2 molecule from Ne + Ne@(4He)N.
A hybrid time dependent quantum dynamics approach [DFT (helium) + quantum wave packet (dopant)] proposed by us (J. Chem. Theory Comput., 2015, 11, 890-906) has been extended to consider bimolecular type reactive processes involving a superfluid helium nanodroplet [A + B@4HeN → AB@4HeN' + (N-N')4He, with A and B being atomic species]; T = 0.37 K. This is probably the first theoretical attempt to study the reaction dynamics of this kind of process and in this initial investigation the total angular momentum has been taken as zero. The Ne + Ne@4HeN → Ne2(v = 0)@4HeN' + (N-N')4He reaction has been considered as the first application example and we have examined the influence of different nanodroplet sizes (N = 200, 500 and 1000) and initial velocities of the outer Ne atom (〈v0〉 = 120-1000 m s-1) on the dynamics. The inner Ne atom produces a greater reduction of the velocity of the outer Ne atom in comparison to what happens in the case of the capture of a Ne atom by a pure nanodroplet. The formation of the Ne2 molecule is a complex phenomenon related to the nature of the helium density waves produced and their reflection from the nanodroplet surface. Though the effective potential energy of Ne2 in the nanodroplet is very different from the gas phase case, the equilibrium Ne-Ne distance is only slightly reduced with respect to the gas phase value, and its vibrational wave function (v = 0) is only modified by 15% with respect to the gas phase one. Furthermore, the analysis of experiments on the capture of Ar, Kr and Xe with larger nanodroplets suggests that the number of evaporated helium atoms obtained here is too low for the initial velocities above 120 m s-1. This problem probably arises from the DFT description of the superfluid helium nanodroplet. We hope that this work will encourage researchers to investigate these very interesting processes about which we still know very little. Lastly, it is worth noting that the quantum treatment presented here can also be applied directly to the study of the photodissociation of an arbitrary diatomic molecule in a superfluid helium nanodroplet.


How research can help control tuberculosis.
Tuberculosis (TB) has played a central role in the history of biomedical science from Koch onwards. Research in the nineteenth and twentieth centuries yielded extremely valuable diagnostic, therapeutic and preventive tools for the control of TB. Following the development of shortcourse chemotherapy in the 1970s and 1980s, research into TB virtually evaporated. Despite the availability of an array of tools, TB control faltered, and the disease remains a major killer. The failure of the fruits of scientific research to control TB is a result of the shortcomings of the tools themselves as well the inadequate application of the tools in populations burdened by TB. A changing epidemiologic situation, with escalating rates of human immunodeficiency virus-related TB and the emergence of multidrug-resistant TB, further threatens global TB control. A robust TB research enterprise will be required to meet the global goals for controlling TB in the twentyfirst century. Basic research is needed to better understand its pathogenesis and immunology, and to identify targets for diagnostics, drugs and vaccines. Research into better biomedical tools to detect, treat and prevent TB is also a major priority, as all of the existing tools have important shortcomings. In addition, research into understanding how to apply both existing and new tools to control TB at the population level is urgently needed. Global funding for TB research, $483 million in 2007, is slowly growing but is far behind need. To meet the ambitious goals of the Global Plan to Stop TB and the Millennium Development Goals, a massive investment in research will be necessary.


A retrospective study of palindrome symmetrical-tip catheters for chronic hemodialysis access in China.
Hemodialysis catheters remain necessary for long-term vascular access in patients for whom arteriovenous access may be problematic or impossible. Developments in catheter design have improved long-term catheter functionality, and reduced the rate of infection and complications associated with their use. This retrospective study of 284 cases of chronic catheterization in 271 patients treated between 2009 and 2011 using Tal Palindrome™ symmetrical-tip (N = 118) or Quinton™ Permcath™ step-tip (N = 166) hemodialysis catheters evaluates the efficacy and the safety of symmetrical-tip dialysis catheters for chronic hemodialysis, compared with a step-tip catheter. Measurements of catheter performance included mean catheter dwell time, incidence of low blood flow, and rates of infection and catheter-related blood stream infection (CRBSI). The symmetrical-tip catheter had a significantly longer mean dwell time compared with the step-tip catheter; 329.4 ± 38.1 versus 273.1 ± 25.4 d (p < 0.05). In addition, the rate of occurrence of low blood flow per 1000 catheter days was lower for the symmetrical-tip compared with the step-tip catheter; 1.13 versus 6.86 (p < 0.01). The symmetrical-tip catheter was also associated with a lower incidence of complications; the rates of infection (0.28 vs. 0.78; p < 0.01) and CRBSI (0.15 vs. 0.44; p < 0.01) were lower compared with those for step-tip catheters, and catheter removal occurred less often for the symmetrical-tip catheter (8% vs. 16%; p < 0.05). The symmetrical-tip hemodialysis catheter was associated with a longer mean dwell time, lower incidence of low blood flow, and lower infection rate compared with the step-tip catheter.


Protective effect of chemically modified SOD on lipid peroxidation and antioxidant status in diabetic rats.
Reactive oxygen species mediated oxidative stress play an important role on the injury of tissue damage and increased attention has been focused on the role of free radicals in diabetes mellitus (DM). In the present study firstly superoxide dismutase (SOD) enzyme was chemically modified with two different polymer and physicochemical properties of these conjugates clearly analyzed. Then, the stability of carboxymethylcellulose-SOD (CMC-SOD) and poly methyl vinyl ether-co-maleic anhydride-SOD (PMVE/MA-SOD) conjugates was investigated against temperature and externally added H2O2. Moreover, we investigated the effect of chemically modified SOD enzyme on lipid peroxidation and antioxidant status in streptozotocin (STZ)-induced diabetic rats. PMVE/MA-SOD conjugate treatment significantly reduced MDA level compared with the control groups, native and CMC-SOD conjugate treated groups in brain, kidney and liver tissue. GSH and SOD enzyme activity in diabetic groups was significantly increased by treatment of CMC-SOD and PMVE/MA-SOD conjugates. The protective effects on degenerative changes in diabetic rats were also further confirmed by histopathological examination. This study provides the preventative activity of SOD-polymer conjugates against complication of oxidative stress in experimentally induced diabetic rats. These results suggest that chemically modified SOD is effective on the oxidative stress-associated disease and offer a therapeutic advantage in clinical use.


Sexual Counseling in Patients With Heart Failure: A Silent Phenomenon: Results From a Convergent Parallel Mixed Method Study.
Patients with heart failure (HF) often worry about resuming sexual activity and may need information. Nurses have a role in helping patients to live with the consequences of HF and can be expected to discuss patients' sexual concerns. The aims of this study were to identify whether nurses discuss consequences of HF on sexuality with patients and to explore their perceived role and barriers regarding this topic. A cross-sectional research design with a convergent parallel mixed method approach was used combining qualitative and quantitative data collected with a self-reported questionnaire. Nurses in this study rarely addressed sexual issues with their patients. The nurses did not feel that discussing sexual concerns with their patients was their responsibility, and only 8% of the nurses expressed confidence to do so. The main phenomenon in discussing sexual concerns seems to be "one of silence": Neither patients nor nurses talk about sexual concerns. Factors influencing this include structural barriers, lack of knowledge and communication skills, as well as relevance of the topic and relationship to patients. Cardiac nurses in Germany rarely practice sexual counseling. It is a phenomenon that is silent. Education and skill-based training might hold potential to "break the silence."


Presynaptic inhibition of identified wind-sensitive afferents in the cercal system of the locust.
The paired cerci located at the tip of the locust abdomen bear a large number of wind-sensitive filiform hairs, each of which sends an axon via the cercal nerve into the terminal ganglion of the CNS. The filiform afferents fire bursts of action potentials when their hairs are displaced by wind or mechanical stimuli. Filiform axon terminals in the CNS are depolarized concomitantly with the discharge of another type of unit (a primary afferent-depolarizing, or PAD, unit) recorded in the cercal nerve. The instantaneous spike frequency of PAD unit discharges matches the evoked depolarization very closely, and during such depolarizations spike amplitudes in the filiform afferent terminals are reduced by up to 55%. Depolarizing current pulses injected into the axonal terminals of an identified filiform afferent evoke spikes that are blocked by the PAD unit, probably via an intercalated interneuron. The PAD unit makes a monosynaptic connection with only one of the 4 giant interneurons (GIN 2) on each side of the terminal ganglion, and indirect connections with 2 others. Depolarizing current pulses injected into the neuropilar segments of GINs evoke fewer spikes when the PAD unit is active, consistent with the PAD unit's mediation of conductance changes in postsynaptic cells. Iontophoretic injection of Lucifer yellow shows the PAD unit to be an afferent with axon terminals overlapping those of filiform afferents and posteriorly directed branches of interneurons such as GIN 2 in the CNS. Passive movements of a cercus, monitored with a position transducer, show that the PAD unit fires discrete bursts during cercal displacement. The PAD unit most probably has its soma and dendrites in tissue spanning the cercal base. By responding to cercal movements sufficient to also activate filiform hairs, and by mediating conductance changes in both the presynaptic terminals of filiform afferents and the postsynaptic membranes of interneurons, the PAD unit desensitizes a pathway to movement-generated afferent input, and ensures that the locust remains sensitive to external wind stimuli.


Control of head lice: past, present and future.
Pediculosis capitis is common among children. Rapid and accurate detection is an underlying principle of effective control and the use of a fine-tooth comb in wet, conditioned hair is most sensitive. However, none of the available treatments are fully effective. Of the current pediculicides available over the counter in the UK, those based on malathion are more effective than pyrethroids. Carbaryl is likely to be the most effective insecticide but is only available on prescription. Wet combing with conditioner has proven to be as effective as some over-the-counter lotions for unsupervised use in the home. There are several promising candidates for new insecticidal actives that are likely to be highly effective for a new generation of pediculicides, as well as a variety of unconventional novel treatments.


Why a successful task substitution in glaucoma care could not be transferred from a hospital setting to a primary care setting: a qualitative study.
Healthcare systems are challenged by a demand that exceeds available resources. One policy to meet this challenge is task substitution-transferring tasks to other professions and settings. Our study aimed to explore stakeholders' perceived feasibility of transferring hospital-based monitoring of stable glaucoma patients to primary care optometrists. A case study was undertaken in the Rotterdam Eye Hospital (REH) using semi-structured interviews and document reviews. They were inductively analysed using three implementation related theoretical perspectives: sociological theories on professionalism, management theories, and applied political analysis. Currently it is not feasible to use primary care optometrists as substitutes for optometrists and ophthalmic technicians working in a hospital-based glaucoma follow-up unit (GFU). Respondents' narratives revealed that: the glaucoma specialists' sense of urgency for task substitution outside the hospital diminished after establishing a GFU that satisfied their professionalization needs; the return on investments were unclear; and reluctant key stakeholders with strong power positions blocked implementation. The window of opportunity that existed for task substitution in person and setting in 1999 closed with the institutionalization of the GFU. Transferring the monitoring of stable glaucoma patients to primary care optometrists in Rotterdam did not seem feasible. The main reasons were the lack of agreement on professional boundaries and work domains, the institutionalization of the GFU in the REH, and the absence of an appropriate reimbursement system. Policy makers considering substituting tasks to other professionals should carefully think about the implementation process, especially in a two-step implementation process (substitution in person and in setting) such as this case. Involving the substituting professionals early on to ensure all stakeholders see the change as a normal step in the professionalization of the substituting professionals is essential, as is implementing the task substitution within the window of opportunity.


Inhibitory effect of deep-sea water on differentiation of 3T3-L1 adipocytes.
Currently, the utilization of deep-sea water (DSW) is receiving much attention due to its high productivity, large quantity, and potential for biological application. The 3T3-L1 cell line is a well-established and commonly used in vitro model to assess adipocyte differentiation. Over the course of several days, confluent 3T3-L1 cells can be converted to adipocytes in the presence of an adipogenic cocktail. In this study, the effects of DSW on differentiation adipocyte 3T3-L1 cells were studied. DSW significantly decreased lipid accumulation, a marker of adipogenesis, in a dose-dependent manner. DSW of hardness 1,000 was the most effective for inhibiting adipocyte differentiation without any cytotoxicity. DSW significantly reduced expression mRNA levels of PPARgamma and C/EBPalpha and protein levels of fatty-acid-binding protein and adiponectin. Our results suggest a potential role for DSW as anti-obesity agents by inhibiting adipocyte differentiation mediated through the down-regulated expression of adipogenic transcription factors and adipocyte-specific proteins.


n-of-1 randomized controlled trials: an opportunity for complementary and alternative medicine evaluation.
Complementary and alternative medicine (CAM) practice has traditionally relied on expert opinion and case examples to evaluate the outcome of a particular therapeutic treatment. Such trials are subject to bias, leading to the formation of erroneous conclusions about the effectiveness of most treatments. This paper reviews the feasibility of n-of-1 trials to better evaluate the clinical and statistical significance of CAM therapies. In particular: (1) problems arising from the use of standard therapeutic trials; (2) the n-of-1 trial and data analysis; (3) clinical use and advantages of the n-of-1 trial in conventional medicine; (4) potential clinical uses of the n-of-1 trial in CAM; (5) preliminary guidelines for the use of the n-of-1 trial in CAM; (6) constraints on the use of the n-of-1 trial in CAM; and (7) ethical issues in the conduct of the n-of-1 trial.


A FACS-optimized screen identifies regulators of genome stability in Candida albicans.
Loss of heterozygosity (LOH) plays important roles in genome dynamics, notably, during tumorigenesis. In the fungal pathogen Candida albicans, LOH contributes to the acquisition of antifungal resistance. In order to investigate the mechanisms that regulate LOH in C. albicans, we have established a novel method combining an artificial heterozygous locus harboring the blue fluorescent protein and green fluorescent protein markers and flow cytometry to detect LOH events at the single-cell level. Using this fluorescence-based method, we have confirmed that elevated temperature, treatment with methyl methanesulfonate, and inactivation of the Mec1 DNA damage checkpoint kinase triggered an increase in the frequency of LOH. Taking advantage of this system, we have searched for C. albicans genes whose overexpression triggered an increase in LOH and identified four candidates, some of which are known regulators of genome dynamics with human homologues contributing to cancer progression. Hence, the approach presented here will allow the implementation of new screens to identify genes that are important for genome stability in C. albicans and more generally in eukaryotic cells.


Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.
Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing. Here, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180-220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406-35,401) sequence reads were obtained per sample, which allowed detection and quantification of minority resistance mutations at amino acid position 181, 184, 188, 190, 210, 215 and 219 in RT. In four of five pre-treatment samples low levels (0.07-0.09%) of the M184I mutation were observed. Other resistance mutations, except T215A and T215I were below the detection limit. During treatment failure, M184V replaced M184I and dominated the population in combination with T215Y, while wild-type variants were rarely detected. Resistant virus disappeared rapidly after treatment interruption and was undetectable as early as after 3 months. In most patients, drug resistant variants were replaced by wild-type variants identical to those present before treatment, suggesting rebound from latent reservoirs. With this highly sensitive UDPS protocol preexisting drug resistance was infrequently observed; only M184I, T215A and T215I were detected at very low levels. Similarly, drug resistant variants in plasma quickly decreased to undetectable levels after treatment interruption. The study gives important insights into the dynamics of the HIV-1 quasispecies and is of relevance for future research and clinical use of the UDPS technology.


OpenSAFELY: Representativeness of electronic health record platform OpenSAFELY-TPP data compared to the population of England.
Background: Since its inception in March 2020, data from the OpenSAFELY-TPP electronic health record platform has been used for more than 20 studies relating to the global COVID-19 emergency. OpenSAFELY-TPP data is derived from practices in England using SystmOne software, and has been used for the majority of these studies. We set out to investigate the representativeness of OpenSAFELY-TPP data by comparing it to national population estimates. Methods: With the approval of NHS England, we describe the age, sex, Index of Multiple Deprivation and ethnicity of the OpenSAFELY-TPP population compared to national estimates from the Office for National Statistics. The five leading causes of death occurring between the 1st January 2020 and the 31st December 2020 were also compared to deaths registered in England during the same period. Results: Despite regional variations, TPP is largely representative of the general population of England in terms of IMD (all within 1.1 percentage points), age, sex (within 0.1 percentage points), ethnicity and causes of death. The proportion of the five leading causes of death is broadly similar to those reported by ONS (all within 1 percentage point). Conclusions: Data made available via OpenSAFELY-TPP is broadly representative of the English population. Users of OpenSAFELY must consider the issues of representativeness, generalisability and external validity associated with using TPP data for health research. Although the coverage of TPP practices varies regionally across England, TPP registered patients are generally representative of the English population as a whole in terms of key demographic characteristics.


Signal transducer and activator of transcription 5b (Stat5b) serine 193 is a novel cytokine-induced phospho-regulatory site that is constitutively activated in primary hematopoietic malignancies.
Signal transducer and activator of transcription 5b (Stat5b) is a critical node in the signaling network downstream of external (cytokines or growth factors) or internal (oncogenic tyrosine kinases) stimuli. Maximum transcriptional activation of Stat5b requires both tyrosine and serine phosphorylation. Although the mechanisms governing tyrosine phosphorylation and activation of Stat5b have been extensively studied, the role of serine phosphorylation remains to be fully elucidated. Using mass spectrometry and phospho-specific antibodies, we identified Ser-193 as a novel site of cytokine-induced phosphorylation within human Stat5b. Stat5b Ser(P)-193 was detected in activated primary human peripheral blood mononuclear cells or lymphoid cell lines in response to several γ common (γc) cytokines, including interleukin (IL)-2, IL-7, IL-9, and IL-15. Kinetic and spatial analysis indicated that Stat5b Ser-193 phosphorylation was rapid and transient and occurred in the cytoplasmic compartment of the cell prior to Stat5b translocation to the nucleus. Moreover, inducible Stat5b Ser-193 phosphorylation was sensitive to inhibitors of mammalian target of rapamycin (mTOR), whereas inhibition of protein phosphatase 2A (PP2A) induced phosphorylation of Ser-193. Reconstitution assays in HEK293 cells in conjunction with site-directed mutagenesis, EMSA, and reporter assays indicated that Ser(P)-193 is required for maximal Stat5b transcriptional activity. Indeed, Stat5b Ser-193 was found constitutively phosphorylated in several lymphoid tumor cell lines as well as primary leukemia and lymphoma patient tumor cells. Taken together, IL-2 family cytokines tightly control Stat5b Ser-193 phosphorylation through a rapamycin-sensitive mechanism. Furthermore, constitutive Ser-193 phosphorylation is associated with Stat5b proto-oncogenic activity and therefore may serve as a novel therapeutic target for treating hematopoietic malignancies.


Coffee, ADORA2A, and CYP1A2: the caffeine connection in Parkinson's disease.
In 1-methyl-4-phenyl 1,2,3,6-tetrahydropyridine animal models of Parkinson's disease (PD), caffeine protects neurons by blocking the adenosine receptor A2A (ADORA2A). Caffeine is primarily metabolized by cytochrome P450 1A2 (CYP1A2). Our objective was to examine whether ADORA2A and CYP1A2 polymorphisms are associated with PD risk or modify the caffeine-PD association. Parkinson's Epidemiology and Genetic Associations Studies in the United States (PEGASUS) included five population-based case-control studies. One laboratory genotyped four ADORA2A and three CYP1A2 polymorphisms in 1325 PD cases and 1735 age- and sex-matched controls. Information regarding caffeine (coffee) consumption and other lifestyle factors came from structured in-person or telephone interviews. Odds ratios (OR) and 95% confidence intervals (CI) were estimated using logistic regression. Two ADORA2A polymorphisms were inversely associated with PD risk - rs71651683, a 5' variant (adjusted allelic OR = 0.51, 95% CI 0.33-0.80, permutation-adjusted P = 0.015) and rs5996696, a promoter region variant (adjusted OR for AC and CC genotypes compared with the AA wild-type genotype were 0.76 (95% CI 0.57-1.02) and 0.37 (95% CI 0.13-1.01), respectively (permutation-adjusted P for trend = 0.04). CYP1A2 polymorphisms were not associated with PD risk; however, the coffee-PD association was strongest among subjects homozygous for either variant allele rs762551 (P(interaction) = 0.05) or rs2470890 (P(interaction) = 0.04). In this consortium study, two ADORA2A polymorphisms were inversely associated with PD risk, but there was weak evidence of interaction with coffee consumption. In contrast, the coffee-PD association was strongest among slow metabolizers of caffeine who were homozygous carriers of the CYP1A2 polymorphisms.


Association of retinol binding protein in multiple-case families with insulin-dependent diabetes.
We performed a family study to investigate the heritability of reduced serum retinol levels observed in type 1 diabetes cases. Diet and serum factors, including retinol, total carotene, malondialdehyde, and retinol binding protein levels, were measured in 11 multiple-case families. The mean serum retinol level of the diabetics (46 ug/dl) was significantly less than the mean serum retinol level of the nondiabetics (60.9 ug/dl). The level of retinol binding protein was also significantly lower in diabetics (6.2 mg/dl) than in nondiabetics (7.6 mg/dl). The serum values of retinol binding protein were closely related within families, including both diabetic and nondiabetic family members. A characteristic shared between diabetics and one-third of their family members was a low ratio of serum retinol to total carotene, suggesting a low conversion of dietary carotene into retinol. Analysis of food frequency reports showed no difference between dietary retinol or total carotene level in diabetics or their relatives. This study offers evidence that heritability and the reduced conversion of carotene may play a role in the level of serum retinol in type 1 diabetes cases.


Computational Modeling of T Cell Hypersensitivity during Coronavirus Infections Leading to Autoimmunity and Lethality.
The human angiotensin-converting enzyme 2 (hACE2) receptor is the primary receptor for SARS-CoV-2 infection. However, the presence of alternative receptors such as the transmembrane glycoprotein CD147 has been proposed as a potential route for SARS-CoV-2 infection. The outcomes of SARS-CoV-2 spike protein binding to receptors have been shown to vary among individuals. Additionally, some patients infected with SARS-CoV-2 develop autoimmune responses. Given that CD147 is involved in the hyperactivation of memory T cells resulting in autoimmunity, we investigated the interaction of the SARS-CoV-2 viral spike protein with CD147 receptor and retinal specific CD147 Ig0 domain in silico using molecular docking and molecular dynamics (MD) simulations. The results indicated that binding involves two critical residues Lys63 and Asp65 in a ubiquitous CD147 isoform, potentially leading to the hyperactivation of T cells for only SARS-CoV-2, but not for SARS-CoV or MERS-CoV. Overall binding was confirmed by docking simulations. Next, MD analyses were completed to verify the docking poses. Polar interactions suggested that the interaction via Lys63 and Asp65 might be one of the determinants associated with severe COVID-19 outcomes. Neither did SARS-CoV nor MERS-CoV bind to these two critical residues when molecular docking analyses were performed. Interestingly, SARS-CoV was able to bind to CD147 with a lower affinity (-4.5 kcal/mol) than SARS-CoV-2 (-5.6 kcal/mol). Furthermore, Delta and Omicron variants of SARS-CoV-2 did not affect the polar interactions with Lys63 and Asp65 in CD147. This study further strengthens the link between SARS-CoV-2 infection and autoimmune responses and provides novel insights for prudent antiviral drug designs for COVID-19 treatment that have implications in the prevention of T cell hyperactivation.


Phylogenetic analyses of "higher" Hamamelididae based on plastid sequence data.
Phylogenetic relationships were examined within the "higher" Hamamelididae using 21 species representing eight families and related outgroups. Chloroplast DNA sequences encoding the matK gene (/1 kilobase) provided 258 informative nucleotide sites. Phylogenetic analysis of this variation produced one most parsimonious tree supporting three monophyletic groups. In this tree, Nothofagus was basal to a well supported clade of remaining "higher" hamamelids, in which Fagaceae, including Fagus, were sister to a clade of core "higher" hamamelids that share wind-pollination, bicarpellate flowers, granular pollen walls, and reduced pollen apertures. Within the core "higher" hamamelids three subclades were resolved, Myricaceae, (Casuarina-(Ticodendron-(Betulaceae))), and (Rhoiptelea-Juglandaceae). Each subclade was well supported but relationships among them were not. The basal position of Nothofagus within the matK tree is consistent with the fossil record of "higher" hamamelids in which Nothofagus pollen appears earlier than microfossils with affinities to other modern "higher" hamamelids. This placement supports the exclusion of Nothofagus from Fagaceae and suggests two hypotheses for the origin of the cupule. The cupule may be ancestral within "higher" hamamelids and subsequently lost in core members of the clade or there may have been two independent origins. It is suggested that the three clades (1) Nothofagaceae, (2) Fagaceae, and (3) Juglandaceae, Rhoiptelea, Myricaceae, Casuarina, Ticodendron, and Betulaceae be considered at the ordinal level and that traditional orders, such as Fagales sensu Cronquist (Fagaceae, Nothofagaceae, and Betulaceae) be abandoned. Comparative analyses of matK sequences with previously published rbcL sequences demonstrate that for the taxa considered here matK sequences produced trees with greater phylogenetic resolution and a higher consistency index.


Mitochondrial DNA rearrangement associated with fertility restoration and cytoplasmic reversion to fertility in cytoplasmic male sterile Phaseolus vulgaris L.
Restoration of pollen fertility to cytoplasmic male sterile (CMS) Phaseolus vulgaris by a nuclear restorer gene provides a system for studying nuclear-cytoplasmic interactions. Introduction of a nuclear restorer gene to this CMS line of P. vulgaris (CMS-Sprite) results in a mitochondrial genome rearrangement similar to that observed upon spontaneous cytoplasmic reversion to fertility. Three spontaneous heritable cytoplasmic revertants were derived from CMS-Sprite. Five fully fertile restored lines were also produced by using restorer line R-351 (BC(3)F(3) populations). Comparison of the mitochondrial DNA restriction patterns of CMS-Sprite, the three fertile revertants, and the five restored lines revealed loss of a 6.0-kilobase (kb) Pst I fragment in all restored and revertant lines. Southern hybridizations with a 1.3-kb BamHI clone, internal to the 6.0-kb Pst I fragment, as a probe revealed two configurations of 6.0-kb homologous sequences in the sterile cytoplasm; one of the configurations was lost upon reversion or restoration. Mitochondrial DNA rearrangement has thus been observed upon restoration by a nuclear restorer gene in this CMS system.


Management of Recurrent Retroperitoneal Sarcoma (RPS) in the Adult: A Consensus Approach from the Trans-Atlantic RPS Working Group.
Retroperitoneal soft tissue sarcomas (RPS) are rare tumors. Surgery is the mainstay of curative therapy, but local recurrence is common. No recommendations concerning the best management of recurring disease have been developed so far. Although every effort should be made to optimize the initial approach, recommendations to treat recurring RPS will be helpful to maximize disease control at recurrence. An RPS transatlantic working group was established in 2013. The goals of the group were to share institutional experiences, build large multi-institutional case series, and develop consensus documents on the approach to this difficult disease. The outcome of this document applies to recurrent RPS that is nonvisceral in origin. Included are sarcomas of major veins, undifferentiated pleomorphic sarcoma of psoas, ureteric leiomyosarcoma (LMS). Excluded are desmoids-type fibromatosis, angiomyolipoma, gastrointestinal stromal tumors, sarcomas arising from the gut or its mesentery, uterine LMS, prostatic sarcoma, paratesticular/spermatic cord sarcoma, Ewing sarcoma, alveolar/embryonal rhabdomyosarcoma, sarcoma arising from teratoma, carcinosarcoma, sarcomatoid carcinoma, clear cell sarcoma, radiation-induced sarcoma, paraganglioma, and malignant pheochromocytoma. Recurrent RPS management was evaluated from diagnosis to follow-up. It is a rare and complex malignancy that is best managed by an experienced multidisciplinary team in a specialized referral center. The best chance of cure is at the time of primary presentation, but some patients may experience prolonged disease control also at recurrence, when the approach is optimized and follows the recommendations contained herein. International collaboration is critical for adding to the present knowledge. A transatlantic prospective registry has been established.


Decision-making in type-B dissection: current evidence and future perspectives.
Aortic dissection is a devastating cardiovascular condition with an incidence of 3,5:100 000. It is classified according to anatomic extent, mechanism of lesion, duration from index event and course (uncomplicated vs. complicated). Intramural hematoma and penetrating aortic ulcers share many of the features of classic dissections, but tend to occur in older patients with advanced atherosclerosis. In uncomplicated type-B dissection, conservative treatment with tight blood pressure and heart rate control is safe and effective. Early stent-graft implantation may, however, result in more favorable aortic remodeling and reduced late complications. For acute complicated cases intervention is usually required. Stent-graft coverage of the entry tear frequently resolves malperfusion, but the role of the false lumen in organ perfusion must be assessed and endovascular revascularization performed if necessary. In chronic type-B dissections, coverage of the entry tear likely results in continued pressurization of the false lumen due to rigidity of the dissecting membrane and distal fenestrations. Better understanding of the different disease mechanisms involved, imaging advances and introduction of dedicated stent-grafts are expected to further improve patient outcomes in the future. Primary and secondary pharmacological prevention, stricter follow-up protocols and screening of family members may also prove valuable. Better patient selection will allow preventive treatment with low morbidity for those at higher risk of complications.


Differences in the clinical manifestations and short-term prognosis of acute cerebral infarction after exposure to Agent Orange.
Agent Orange (AO) is the code name for one of the herbicides and defoliants used in the Vietnam War. Studies conducted thus far show a significant correlation between AO and the occurrence of cardiovascular diseases. But there is little data on the association between AO and stroke, and limited studies have targeted patient groups exposed to AO. Bohun medical center Institutional Review Board (IRB) approved the study. (ID: 341) We studied patients with acute ischemic stroke within 7 days of onset in VHS medical center and 4 other general hospitals. Among them, 91 consecutive patients with previous exposure to AO were evaluated. For controlled group, 288 patients with no history of AO exposure were chosen. There were 49 (44.0 %) DM patient with a higher frequency in the exposure group (93 (32.3 %) in control P = 0.045). There were 6 (6.6 %) hyperlipidemia in exposure group and 69 (24.0 %) in control. (P < 0.002). Small vessel occlusion was the most common subtype (36, 39.6 %) in exposure group but in control group, the large artery atherosclesosis was (120, 41.7 %) (P = 0.014). The NIHSS of the exposure group on admission showed lower scores (median values, 2 and 4, respectively; P = 0.003). The median mRS was 1 for the exposure group and 2 for the control group, at discharge and after 3 months. After 3 months of discharge, 55 (60.4 %) in the exposure group and 171 (59.4 %) in the control group showed below mRS 1 (P = 0.001). This study targeted patients who are Vietnam veteran. There is some difference in vascular risk factors and clinical manifestations suggest AO exposure has contributed to a certain extent to the stroke.


Neural expression of the transcription factor THAP1 during development in rat.
Loss of function mutations in THAP1 has been associated with primary generalized and focal dystonia in children and adults. THAP1 encodes a transcription factor (THAP1) that harbors an atypical zinc finger domain and plays a critical role in G(1)-S cell cycle control. Current thinking suggests that dystonia may be a neurodevelopmental circuit disorder. Hence, THAP1 may participate in the development of the nervous system. Herein, we report the neurodevelopmental expression patterns of Thap1 transcript and THAP1 protein from the early postnatal period through adulthood in the rat brain, spinal cord and dorsal root ganglia (DRG). We detected Thap1 transcript and THAP1-immunoreactivity (IR) in the cerebral cortex, cerebellum, striatum, substantia nigra, thalamus, spinal cord and DRG. Thap1 transcript expression was higher in the brain than in spinal cord and DRG at P1 and P7 and declined to similar levels at P14 and later time points in all regions except the cerebellum, where it remained high through adulthood. In the brain, THAP1 expression was highest in early development, particularly in the cerebellum at P7. In addition to Purkinje cells in the cerebellum, THAP1-IR was also localized to pyramidal neurons in the cerebral cortex, relay neurons in the thalamus, medium spiny and cholinergic neurons in the striatum, dopaminergic neurons in the substantia nigra, and pyramidal and interneurons in the hippocampus. In the cerebellar cortex, THAP1-IR was prominently distributed in the perikarya and proximal dendrites of Purkinje cells at early time-points. In contrast, it was more diffusely distributed throughout the dendritic arbor of adult Purkinje cells producing a moderate diffuse staining pattern in the molecular layer. At all time points, nuclear IR was weaker than cytoplasmic IR. The prominent cytoplasmic and developmentally regulated expression of THAP1 suggests that THAP1 may function as part of a cell surface-nucleus signaling cascade involved in terminal neural differentiation.


A randomized trial of a multicomponent intervention for adolescent sun protection behaviors.
To evaluate a multicomponent primary care-based intervention to increase sun protection behaviors among adolescents. Excessive sun exposure in childhood increases the lifetime risk of melanomas and other forms of skin cancer. Interventions to improve sun protection behaviors in childhood have been based primarily in school and community settings, with little attention to the role of primary care physicians. A 2-year randomized controlled trial. Primary care physician offices and participant homes. Eight hundred nineteen adolescents aged 11 to 15 years. At the study onset and the 12-month follow-up, the adolescents engaged in an office-based expert system assessment of sun protection behaviors followed by brief stage-based counseling from the primary care provider. Participants also received up to 6 expert system-generated feedback reports, a brief printed manual, and periodic mailed tip sheets. Participants randomized to the comparison condition received a physical activity and nutrition intervention. A self-reported composite measure of sun protection behavior. A random-effects repeated-measures model indicated a greater adoption of sun protection behaviors over time in the intervention group compared with the control group. The intervention effect corresponded to between-group differences at 24 months in avoiding the sun and limiting exposure during midday hours and using sunscreen with a sun protection factor of at least 15. Secondary analysis indicated that, by 24 months, more adolescents in the intervention group had moved to the action or the maintenance stage of change than those in the control group (25.1% vs 14.9%; odds ratio, 1.74; 95% confidence interval, 1.13-2.68). Sun protection behavior was also found to be positively associated with the completion of more intervention sessions (P = .002). Primary care counseling coupled with a minimal-intensity expert system intervention can improve adolescents' sun protection behaviors.


Effects of ciglitazone on blood pressure and intracellular calcium metabolism.
Ciglitazone is the prototype of the thiazolidinedione class of compounds currently being developed for the treatment of insulin resistance and non-insulin-dependent diabetes. The effects of thiazolidinediones on blood pressure and cell calcium metabolism are not well defined. In the obese Zucker rat, a widely studied model of insulin resistance associated with mild hypertension, we investigated the effects of ciglitazone on plasma insulin levels and mean arterial pressure. We also evaluated the effects of ciglitazone on the changes in cytosolic calcium induced by platelet-derived growth factor in A172 human glioblastoma cells and rat A10 vascular smooth muscle cells. Oral administration of ciglitazone, approximately 45 mg/kg per day for 4 weeks, induced significant reductions in plasma insulin levels (p < 0.001) and blood pressure (p < 0.05). Ciglitazone was also found to significantly attenuate the capacity of platelet-derived growth factor BB homodimer to induce sustained increases in intracellular free calcium. These findings suggest that thiazolidinediones may offer a novel pharmacological approach to the treatment of hypertension, and raise the possibility that these compounds may affect blood pressure not only by affecting insulin metabolism but also by modifying the cell calcium response to pressor agents, growth factors, or both.


Protocol for secondary data analysis of 4 UK cohorts examining youth adversity and mental health in the context of intersectionality.
Youth adversity (e.g., abuse and bullying victimisation) is robust risk factor for later mental health problems (e.g., depression and anxiety). Research shows the prevalence of youth adversity and rates of mental health problems vary by individual characteristics, identity or social groups (e.g., gender and ethnicity). However, little is known about whether the impact of youth adversity on mental health problems differ across the intersections of these characteristics (e.g., white females). This paper reports on a component of the ATTUNE research programme (work package 2) which aims to investigate the impact and mechanisms of youth adversity on depressive and anxiety symptoms in young people by intersectionality profiles. The data are from 4 UK adolescent cohorts: HeadStart Cornwall, Oxwell, REACH, and DASH. These cohorts were assembled for adolescents living in distinct geographical locations representing coastal, suburban and urban places in the UK. Youth adversity was assessed using a series of self-report questionnaires and official records. Validated self-report instruments measured depressive and anxiety symptoms. A range of different variables were classified as possible social and cognitive mechanisms. Structural equation modelling (e.g., multiple group models, latent growth models) and multilevel modelling will be used, with adaptation of methods to suit the specific available data, in accord with statistical and epidemiological conventions. The results from this research programme will broaden our understanding of the association between youth adversity and mental health, including new information about intersectionality and related mechanisms in young people in the UK. The findings will inform future research, clinical guidance, and policy to protect and promote the mental health of those most vulnerable to the negative consequences of youth adversity.


A high-wavenumber boundary-element method for an acoustic scattering problem.
In this paper we show stability and convergence for a novel Galerkin boundary-element-method approach to the impedance boundary-value problem for the Helmholtz equation in a half-plane with piecewise constant boundary data. This problem models, for example, outdoor sound propagation over inhomogeneous flat terrain. To achieve a good approximation with a relatively low number of degrees of freedom we employ a graded mesh with smaller elements adjacent to discontinuities in impedance, and a special set of basis functions for the Galerkin method so that, on each element, the approximation space consists of polynomials (of degree nu) multiplied by traces of plane waves on the boundary. In the case where the impedance is constant outside an interval [a,b], which only requires the discretization of [a,b], we show theoretically and experimentally that the L(2) error in computing the acoustic field on [a,b] is O(log(nu+3/2)|k(b-a)|M(-(nu+1)), where M is the number of degrees of freedom and k is the wavenumber. This indicates that the proposed method is especially commendable for large intervals or a high wavenumber. In a final section we sketch how the same methodology extends to more general scattering problems.


Immunogenecity of modified alkane polymers is mediated through TLR1/2 activation.
With the advancement of biomedical technology, artificial materials have been developed to replace diseased, damaged or nonfunctional body parts. Among such materials, ultra high molecular weight alkane or modified alkyl polymers have been extensively used in heart valves, stents, pacemakers, ear implants, as well as total joint replacement devices. Although much research has been undertaken to design the most non-reactive biologically inert polyethylene derivatives, strong inflammatory responses followed by rejection and failure of the implant have been noted. Purification of the alkane polymers from the site of inflammation revealed extensive "in vivo" oxidation as detected by fourier transformed infra-red spectroscopy. Herein, we report the novel observation that oxidized alkane polymers induced activation of TLR1/2 pathway as determined by ligand dependent changes in intrinsic tyrosine fluorescence intensity and NF-kappaB luciferase gene assays. Oxidized polymers were very effective in activating dendritic cells and inducing secretion of pro-inflammatory cytokines. Molecular docking of the oxidized alkanes designated ligand specificity and polymeric conformations fitting into the TLR1/2 binding grooves. This is the first report of a synthetic polymer activating immune responses through TLR binding.


Isolation and characterization of a c-type lysozyme from the nurse shark.
Lysozyme is a ubiquitous antibacterial enzyme that occurs in numerous invertebrate and vertebrate species. Three forms have been described c-type, g-type and i-type which differ in primary structure. Shark lysozyme has not been characterized; here we report on the isolation and characterization of lysozyme from unstimulated shark (Ginglymostoma cirratum) leukocytes and provide amino acid sequence data across the highly conserved active site of the molecule identifying it to be a c-type lysozyme. A leukocyte lysate was applied either (a) to the first of two sequential DE-52 cellulose columns or alternatively, (b) to a DEAE-Sepharose column. Lysozyme activity in lysate and active fractions was identified by zones of lysis of Micrococcus lysodeikticus cell walls on lysoplates and zones of growth inhibition in agar diffusion assays using Planococcus citreus as the target organism. SDS-PAGE analysis revealed a 14 kDa protein which was identified as lysozyme by mass spectroscopic analysis of peptides, reactivity against anti-HEWL antibodies on a Western blot, hydrolysis of M. lysodeikticus cell walls, and inhibition of growth of P. citreus on AU-gel blots in which the area of growth inhibition correlated to a 14 kDa protein.


Albusnodin: an acetylated lasso peptide from Streptomyces albus.
We describe a lasso peptide, albusnodin, that is post-translationally modified with an acetyl group, the first example of a lasso peptide with this modification. Using heterologous expression, we further show that the acetyltransferase colocalized with the albusnodin gene cluster is required for the biosynthesis of this lasso peptide. This type of lasso peptide is widespread in Actinobacteria with 44 examples found in currently sequenced genomes.


Predicting prokaryotic ecological niches using genome sequence analysis.
Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as 'mountains' on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a "niche map", to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence.


Uncoupling of EphA/ephrinA signaling and spontaneous activity in neural circuit wiring.
Classic studies have proposed that genetically encoded programs and spontaneous activity play complementary but independent roles in the development of neural circuits. Recent evidence, however, suggests that these two mechanisms could interact extensively, with spontaneous activity affecting the expression and function of guidance molecules at early developmental stages. Here, using the developing chick spinal cord and the mouse visual system to ectopically express the inwardly rectifying potassium channel Kir2.1 in individual embryonic neurons, we demonstrate that cell-intrinsic blockade of spontaneous activity in vivo does not affect neuronal identity specification, axon pathfinding, or EphA/ephrinA signaling during the development of topographic maps. However, intrinsic spontaneous activity is critical for axon branching and pruning once axonal growth cones reach their correct topographic position in the target tissues. Our experiments argue for the dissociation of spontaneous activity from hard-wired developmental programs in early phases of neural circuit formation.


Outbreeding effects in an inbreeding insect, Cimex lectularius.
In some species, populations with few founding individuals can be resilient to extreme inbreeding. Inbreeding seems to be the norm in the common bed bug, Cimex lectularius, a flightless insect that, nevertheless, can reach large deme sizes and persist successfully. However, bed bugs can also be dispersed passively by humans, exposing inbred populations to gene flow from genetically distant populations. The introduction of genetic variation through this outbreeding could lead to increased fitness (heterosis) or be costly by causing a loss of local adaptation or exposing genetic incompatibility between populations (outbreeding depression). Here, we addressed how inbreeding within demes and outbreeding between distant populations impact fitness over two generations in this re-emerging public health pest. We compared fitness traits of families that were inbred (mimicking reproduction following a founder event) or outbred (mimicking reproduction following a gene flow event). We found that outbreeding led to increased starvation resistance compared to inbred families, but this benefit was lost after two generations of outbreeding. No other fitness benefits of outbreeding were observed in either generation, including no differences in fecundity between the two treatments. Resilience to inbreeding is likely to result from the history of small founder events in the bed bug. Outbreeding benefits may only be detectable under stress and when heterozygosity is maximized without disruption of coadaptation. We discuss the consequences of these results both in terms of inbreeding and outbreeding in populations with genetic and spatial structuring, as well as for the recent resurgence of bed bug populations.


PAS domains: internal sensors of oxygen, redox potential, and light.
PAS domains are newly recognized signaling domains that are widely distributed in proteins from members of the Archaea and Bacteria and from fungi, plants, insects, and vertebrates. They function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. Specificity in sensing arises, in part, from different cofactors that may be associated with the PAS fold. Transduction of redox signals may be a common mechanistic theme in many different PAS domains. PAS proteins are always located intracellularly but may monitor the external as well as the internal environment. One way in which prokaryotic PAS proteins sense the environment is by detecting changes in the electron transport system. This serves as an early warning system for any reduction in cellular energy levels. Human PAS proteins include hypoxia-inducible factors and voltage-sensitive ion channels; other PAS proteins are integral components of circadian clocks. Although PAS domains were only recently identified, the signaling functions with which they are associated have long been recognized as fundamental properties of living cells.


Regioselective Diels-Alder reaction to open-cage ketolactam derivatives of C60.
Open-cage ketolactam fullerenes reacted with dienes on the rim of the orifice both regio- and stereoselectively. Unequivocal evidence for the structure of the Diels-Alder adduct was provided by 2D INADEQUATE 13C NMR studies on 13C enriched material, as well as via DFT-GIAO calculations. The theoretical calculations successfully model the regioselective and the endo stereoselective reaction, predicting molecular orbital control along with a repulsive steric interaction between the substituents on the nitrogen atom and those on the diene.


Effect of cocoa on blood pressure.
High blood pressure is an important risk factor for cardiovascular disease attributing to about 50% of cardiovascular events worldwide and 37% of cardiovascular related deaths in Western populations. Epidemiological studies suggest that cocoa rich products reduce the risk of cardiovascular disease. Flavanols found in cocoa have been shown to increase the formation of endothelial nitric oxide which promotes vasodilation and therefore blood pressure reduction. Previous meta-analyses have shown that cocoa-rich foods may reduce blood pressure. Recently additional trials had conflicting results. To determine the effect of flavanol-rich chocolate or cocoa products on blood pressure in people with or without hypertension. We searched the following electronic databases from inception to November 2011: Cochrane Hypertension Group Specialised Register, CENTRAL, MEDLINE and EMBASE. In addition we searched international trial registries, and the reference lists of review articles and included trials. Randomised controlled trials (RCT) investigating the effects of chocolate or cocoa products on systolic and diastolic blood pressure in adults for a minimum of two weeks duration. Two authors independently extracted data and assessed the risk of bias in each trial in consultation with a third author. Random effects meta-analyses on all studies fitting the inclusion criteria were conducted using Review Manager version 5.1 and Stata version 12. Heterogeneity was explored by subgroup analyses and univariate meta-regression analysis of several variables including dosage of flavanol content (total or monomers) in chocolate or cocoa products, blinding, baseline blood pressure, theobromine content, sugar content, body-mass-index (BMI), duration and age. Twenty studies met the inclusion criteria. Meta-analyses of the 20 studies involving 856 mainly healthy participants revealed a statistically significant blood pressure reducing effect of flavanol-rich cocoa products compared with control in short-term trials of 2-18 weeks duration: Mean difference SBP (95%CI): -2.77 (-4.72, -0.82) mm Hg, p=0.005, n=20; mean difference DBP (95%CI): - 2.20 (-3.46, -0.93) mm Hg, p=0.006, n=19 available for DBP.Trials provided participants with 30-1080 mg of flavanols (mean=545.5 mg) in 3.6-105 g of cocoa products per day in the active intervention group. In half of the trials (n=10) the active group consumed 500-750 mg of flavanols per day. The control group received either a flavanol-free product (n=12) or a low-flavanol containing cocoa powder (6.4 and 41 mg flavanols, n=8). Subgroup meta-analysis of trials with a flavanol-free control group revealed a significant blood pressure reducing effect, in contrast to trials using a low-flavanol product in the control group. This analysis may have been confounded by trial duration and the level of blinding of participants.Trial duration was short (mean 4.4 weeks, range 2-8 weeks, n=19, and one trial of 18 weeks). A significant blood pressure reducing effect was evident in trials of 2 weeks duration (n=9), but not in trials of >2 weeks duration (n=11). It is important to note that seven out of the nine trials (78%) of 2 weeks duration also had a flavanol-free control group. Therefore, subgroup analysis by duration might be confounded by flavanol dosage used in the control groups, and the level of blinding of participants.Adverse effects including gastrointestinal complaints and distaste of the trial product were reported by 5% of patients in the active cocoa intervention group and 1% of patients in the control groups. Flavanol-rich chocolate and cocoa products may have a small but statistically significant effect in lowering blood pressure by 2-3 mm Hg in the short term.Our findings are limited by the heterogeneity between trials, which was explored by univariate meta-regression and subgroup analyses. Subgroup meta-analysis of trials using a flavanol-free control group revealed a significant blood pressure reducing effect of cocoa, whereas analysis of trials using a low-flavanol control product did not. While it appears that shorter trials of 2 weeks duration were more effective, analysis may be confounded by type of control and unblinding of participants, as the majority of 2-week trials also used a flavanol-free control and unblinding of participants. Results of these and other subgroup analyses based on, for example, age of participants, should be interpreted with caution and need to be confirmed or refuted in trials using direct randomized comparison.Long-term trials investigating the effect of cocoa products are needed to determine whether or not blood pressure is reduced on a chronic basis by daily ingestion of cocoa. Furthermore, long-term trials investigating the effect of cocoa on clinical outcomes are also needed to assess whether cocoa has an effect on cardiovascular events and to assess potential adverse effects associated with chronic ingestion of cocoa products.


Predicting drug resistance evolution: insights from antimicrobial peptides and antibiotics.
Antibiotic resistance constitutes one of the most pressing public health concerns. Antimicrobial peptides (AMPs) of multicellular organisms are considered part of a solution to this problem, and AMPs produced by bacteria such as colistin are last-resort drugs. Importantly, AMPs differ from many antibiotics in their pharmacodynamic characteristics. Here we implement these differences within a theoretical framework to predict the evolution of resistance against AMPs and compare it to antibiotic resistance. Our analysis of resistance evolution finds that pharmacodynamic differences all combine to produce a much lower probability that resistance will evolve against AMPs. The finding can be generalized to all drugs with pharmacodynamics similar to AMPs. Pharmacodynamic concepts are familiar to most practitioners of medical microbiology, and data can be easily obtained for any drug or drug combination. Our theoretical and conceptual framework is, therefore, widely applicable and can help avoid resistance evolution if implemented in antibiotic stewardship schemes or the rational choice of new drug candidates.


Prospective acceleration of diffusion tensor imaging with compressed sensing using adaptive dictionaries.
Diffusion MRI requires acquisition of multiple diffusion-weighted images, resulting in long scan times. Here, we investigate combining compressed sensing and a fast imaging sequence to dramatically reduce acquisition times in cardiac diffusion MRI. Fully sampled and prospectively undersampled diffusion tensor imaging data were acquired in five rat hearts at acceleration factors of between two and six using a fast spin echo (FSE) sequence. Images were reconstructed using a compressed sensing framework, enforcing sparsity by means of decomposition by adaptive dictionaries. A tensor was fit to the reconstructed images and fiber tractography was performed. Acceleration factors of up to six were achieved, with a modest increase in root mean square error of mean apparent diffusion coefficient (ADC), fractional anisotropy (FA), and helix angle. At an acceleration factor of six, mean values of ADC and FA were within 2.5% and 5% of the ground truth, respectively. Marginal differences were observed in the fiber tracts. We developed a new k-space sampling strategy for acquiring prospectively undersampled diffusion-weighted data, and validated a novel compressed sensing reconstruction algorithm based on adaptive dictionaries. The k-space undersampling and FSE acquisition each reduced acquisition times by up to 6× and 8×, respectively, as compared to fully sampled spin echo imaging. Magn Reson Med 76:248-258, 2016. © 2015 Wiley Periodicals, Inc.


The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification.
Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.


Prenylated proteins: the structure of the isoprenoid group.
The mevalonate-derived portion of a prenylated protein from Chinese hamster ovary cells has been established as diterpenoid (C20). This group is linked to a carboxyl-terminal cysteine as a thioether. It was removed from the protein by hydrazinolysis followed by Raney nickel desulfurization, and the resulting hydrocarbon fraction was analyzed by gas chromatography-mass spectrometry.


Drug resistance in leishmaniasis.
Leishmaniasis is a complex disease, with visceral and cutaneous manifestations, and is caused by over 15 different species of the protozoan parasite genus Leishmania. There are significant differences in the sensitivity of these species both to the standard drugs, for example, pentavalent antimonials and miltefosine, and those on clinical trial, for example, paromomycin. Over 60% of patients with visceral leishmaniasis in Bihar State, India, do not respond to treatment with pentavalent antimonials. This is now considered to be due to acquired resistance. Although this class of drugs has been used for over 60 years for leishmaniasis treatment, it is only in the past 2 years that the mechanisms of action and resistance have been identified, related to drug metabolism, thiol metabolism, and drug efflux. With the introduction of new therapies, including miltefosine in 2002 and paromomycin in 2005-2006, it is essential that there be a strategy to prevent the emergence of resistance to new drugs; combination therapy, monitoring of therapy, and improved diagnostics could play an essential role in this strategy.


A shrimp glycosylase protein, PmENGase, interacts with WSSV envelope protein VP41B and is involved in WSSV pathogenesis.
Viral glycoproteins are expressed by many viruses, and during infection they usually play very important roles, such as receptor attachment or membrane fusion. The mature virion of the white spot syndrome virus (WSSV) is unusual in that it contains no glycosylated proteins, and there are currently no reports of any glycosylation mechanisms in the pathogenesis of this virus. In this study, we cloned a glycosylase, mannosyl-glycoprotein endo-β-N-acetylglucosaminidase (ENGase, EC 18.104.22.168), from Penaeus monodon and found that it was significantly up-regulated in WSSV-infected shrimp. A yeast two-hybrid assay showed that PmENGase interacted with both structural and non-structural proteins, and GST-pull down and co-immunoprecipitation (Co-IP) assays confirmed its interaction with the envelope protein VP41B. In the WSSV challenge tests, the cumulative mortality and viral copy number were significantly decreased in the PmEngase-silenced shrimp, from which we conclude that shrimp glycosylase interacts with WSSV in a way that benefits the virus. Lastly, we speculate that the deglycosylation activity of PmENGase might account for the absence of glycosylated proteins in the WSSV virion.


Cataleptic effects of gamma-hydroxybutyrate (GHB), its precursor gamma-butyrolactone (GBL), and GABAB receptor agonists in mice: differential antagonism by the GABAB receptor antagonist CGP35348.
Gamma-hydroxybutyrate (GHB) is used to treat narcolepsy but is also abused. GHB has many actions in common with the GABA(B) receptor agonist baclofen. To further study the role of GABA(B) receptors in the effects of GHB. The experiments examined the ability of the GABA(B) receptor antagonist CGP35348 to attenuate GHB-induced catalepsy in comparison with its ability to attenuate the cataleptic effects of GABA(B) receptor agonists. In C57BL/6J mice, GHB, the GHB precursor gamma-butyrolactone (GBL), and the GABA(B) receptor agonists baclofen and SKF97541 all produced catalepsy but differed in potency (i.e., SKF97541>baclofen>GBL>GHB) and in onset of action. The cataleptic effects of drug combinations were assessed at the time of peak effect of each compound, i.e., 60 min after CGP35348 and 60, 30, 30, and 15 min after baclofen, SKF97541, GHB, and GBL, respectively. At 100 mg/kg, CGP35348 shifted the dose-response curves of baclofen and SKF97541 to the right but not those of GHB and GBL; at 320 mg/kg, CGP35348 shifted the curves of all four compounds to the right. The finding that CGP35348 was about threefold less potent to antagonize GHB and GBL than baclofen and SKF97541 is further evidence that the mechanisms mediating the effects of GHB and GABA(B) agonists are not identical. Differential involvement of GABA(B) receptor subtypes, or differential interactions with GABA(B) receptors, may possibly explain why GHB is effective for treating narcolepsy and is abused whereas baclofen is not.


Decreased miR-340 expression in bone marrow is associated with liver metastasis of colorectal cancer.
Studies have shown the prognostic significance of disseminated tumor cells (DTC) in bone marrow of patients with colorectal cancer. However, the molecular characteristics of DTCs, including their miRNA expression profiles, remain mostly unknown. In this study, we analyzed the miRNA expression of DTCs in bone marrow. EpCAM(+) bone marrow cells were collected using immunomagnetic beads after exclusion of CD14(+) and CD45(+) cells, then subjected to miRNA microarray analysis. Cluster analysis (7 colorectal cancer patients with liver metastasis and 12 colorectal cancer patients without liver metastasis) indicated that miR-340 and miR-542-3p expressions were significantly decreased in EpCAM(+) bone marrow cells of patients with liver metastasis (P = 0.019 and 0.037, respectively). We demonstrated that pre-miR-340 administration inhibited growth of colon cancer cells and suppressed c-Met expression in vitro. In clinical samples of colorectal cancer, miR-340 was expressed at significantly lower levels in tumor tissues compared with normal mucosa. Survival analysis in 136 patients with colorectal cancer indicated that low miR-340 expression was correlated with shorter 5-year disease-free survival (P = 0.023) and poor 5-year overall survival (P = 0.046). It was of note that the colorectal cancer group with low miR-340 and high c-Met expression had the worst prognosis. We further demonstrated that systemic pre-miR-340 administration suppressed growth of pre-established HCT116 tumors in animal therapeutic models. These findings indicate that miR-340 may be useful as a novel prognostic factor and as a therapeutic tool against colorectal cancer. Our data suggest that miR-340 in bone marrow may play an important role in regulating the metastasis cascade of colorectal cancer.


Encoding of sequence boundaries in the subthalamic nucleus of patients with Parkinson's disease.
Sequential behaviour is widespread not only in humans but also in animals, ranging in different degrees of complexity from locomotion to birdsong or music performance. The capacity to learn new motor sequences relies on the integrity of basal ganglia-cortical loops. In Parkinson's disease the execution of habitual action sequences as well as the acquisition of novel sequences is impaired partly due to a deficiency in being able to generate internal cues to trigger movement sequences. In addition, patients suffering from Parkinson's disease have difficulty initiating or terminating a self-paced sequence of actions. Direct recordings from the basal ganglia in these patients show an increased level of beta (14-30 Hz) band oscillatory activity associated with impairment in movement initiation. In this framework, the current study aims to evaluate in patients with Parkinson's disease the neuronal activity in the subthalamic nucleus related to the encoding of sequence boundaries during the explicit learning of sensorimotor sequences. We recorded local field potential activity from the subthalamic nucleus of 12 patients who underwent deep brain stimulation for the treatment of advanced Parkinson's disease, while the patients in their usual medicated state practiced sequences of finger movements on a digital piano with corresponding auditory feedback. Our results demonstrate that variability in performance during an early phase of sequence acquisition correlates across patients with changes in the pattern of subthalamic beta-band oscillations; specifically, an anticipatory suppression of beta-band activity at sequence boundaries is linked to better performance. By contrast, a more compromised performance is related to attenuation of beta-band activity before within-sequence elements. Moreover, multivariate pattern classification analysis reveals that differential information about boundaries and within-sequence elements can be decoded at least 100 ms before the keystroke from the amplitude of oscillations of subthalamic nucleus activity across different frequency bands, not just from the beta-band. Additional analysis was performed to assess the strength of how much the putative signal encoding class of ordinal position (boundaries, within-sequence elements) is reflected in each frequency band. This analysis demonstrates that suppression of power in the beta-band contains the most class-related information, whereas enhancement of gamma band (31-100 Hz) activity is the second main contributor to the encoding. Our findings support the hypothesis that subthalamic nucleus-mediated gating of salient boundary elements during sequence encoding may be a prerequisite for the adequate acquisition of action sequences and the transition to habitual behaviour.


Validation of weighed records and other methods of dietary assessment using the 24 h urine nitrogen technique and other biological markers.
Results from analysis of 24 h urine collections, verified for completeness with para-amino benzoic acid, and blood samples collected over 1 year were compared with 16 d weighed records of all food consumed collected over the year, and with results from 24 h recalls, food-frequency questionnaires and estimated food records in 160 women. Using the weighed records, individuals were sorted into quintiles of the distribution of the urine N excretion:dietary N intake ratio (UN:DN). UN exceeded DN in the top quintile of this ratio; mean ratio UN:DN = 1.13. Individuals in this top quintile were heavier, had significantly greater body mass indices, were reportedly more restrained eaters, had significantly lower energy intake:basal metabolic rate ratios (EI:BMR), and had correlated ratios of UN:DN and EI:BMR (r -0.62). Those in the top quintile reported lower intakes of energy and energy-yielding nutrients, Ca, fats, cakes, breakfast cereals, milk and sugars than individuals in the other quintiles but not lower intakes of non-starch polysaccharides, vitamin C, vegetables, potatoes or meat. Correlations between dietary intake from weighed records and 24 h urine K were 0.74 and 0.82, and between dietary vitamin C and beta-carotene and plasma vitamin C and beta-carotene 0.86 and 0.48. Correlations between dietary N intake from weighed records and 24 h urine excretion were high (0.78-0.87). Those between N from estimated food records and urine N were r 0.60-0.70. Correlations between urine N and 24 h recalls and food-frequency questionnaires were in the order of 0.01 to 0.5. Despite problems of underreporting in overweight individuals in 20% of this sample, weighed records remained the most accurate method of dietary assessment, and only an estimated 7 d diary was able to approach this accuracy.


An analysis of the use of genomic DNA as a universal reference in two channel DNA microarrays.
DNA microarray is an invaluable tool for gene expression explorations. In the two-dye microarray, fluorescence intensities of two samples, each labeled with a different dye, are compared after hybridization. To compare a large number of samples, the 'reference design' is widely used, in which all RNA samples are hybridized to a common reference. Genomic DNA is an attractive candidate for use as a universal reference, especially for bacterial systems with a low percentage of non-coding sequences. However, genomic DNA, comprising of both the sense and anti-sense strands, is unlike the single stranded cDNA usually used in microarray hybridizations. The presence of the antisense strand in the 'reference' leads to reactions between complementary labeled strands in solution and may cause the assay result to deviate from true values. We have developed a mathematical model to predict the validity of using genomic DNA as a reference in the microarray assay. The model predicts that the assay can accurately estimate relative concentrations for a wide range of initial cDNA concentrations. Experimental results of DNA microarray assay using genomic DNA as a reference correlated well to those obtained by a direct hybridization between two cDNA samples. The model predicts that the initial concentrations of labeled genomic DNA strands and immobilized strands, and the hybridization time do not significantly affect the assay performance. At low values of the rate constant for hybridization between immobilized and mobile strands, the assay performance varies with the hybridization time and initial cDNA concentrations. For the case where a microarray with immobilized single strands is used, results from hybridizations using genomic DNA as a reference will correspond to true ratios under all conditions. Simulation using the mathematical model, and the experimental study presented here show the potential utility of microarray assays using genomic DNA as a reference. We conclude that the use of genomic DNA as reference DNA should greatly facilitate comparative transcriptome analysis.


How Metamorphosis Is Different in Plethodontids: Larval Life History Perspectives on Life-Cycle Evolution.
Plethodontid salamanders exhibit biphasic, larval form paedomorphic, and direct developing life cycles. This diversity of developmental strategies exceeds that of any other family of terrestrial vertebrate. Here we compare patterns of larval development among the three divergent lineages of biphasic plethodontids and other salamanders. We discuss how patterns of life-cycle evolution and larval ecology might have produced a wide array of larval life histories. Compared with many other salamanders, most larval plethodontids have relatively slow growth rates and sometimes exceptionally long larval periods (up to 60 mo). Recent phylogenetic analyses of life-cycle evolution indicate that ancestral plethodontids were likely direct developers. If true, then biphasic and paedomorphic lineages might have been independently derived through different developmental mechanisms. Furthermore, biphasic plethodontids largely colonized stream habitats, which tend to have lower productivity than seasonally ephemeral ponds. Consistent with this, plethodontid larvae grow very slowly, and metamorphic timing does not appear to be strongly affected by growth history. On the basis of this, we speculate that feeding schedules and stress hormones might play a comparatively reduced role in governing the timing of metamorphosis of stream-dwelling salamanders, particularly plethodontids.


Eltrombopag in children with severe aplastic anemia.
Immunosuppressive therapy with horse antithymocyte globulin and cyclosporine currently remains the standard therapy for children with severe aplastic anemia (SAA) who lack human leukocyte antigen (HLA)-identical sibling. The thrombopoietin receptor agonist eltrombopag has been recently approved for SAA patients 2 years and older. However, there are limited data on its safety and efficacy in pediatric cohorts. We conducted a retrospective study of patients ≤18 years old consecutively diagnosed with SAA between 2000 and 2018. Patients received either standard immunosuppressive therapy (IST-Std) or IST with eltrombopag (IST-Epag). The primary outcome was the objective response (OR), including partial and complete response (CR), at 6 and 12 months after starting therapy. We identified 16 patients receiving IST-Std and nine IST-Epag treatment (seven of nine as upfront therapy and two of seven after previously failed IST). The OR at 6 and 12 months in IST-Std arm was 71% and 100%, with CR in 29% and 58%, respectively. Seven patients receiving upfront IST-Epag had OR at 6 and 12 months, with two of seven (29%) achieving CR at 6 and 12 months. Two patients who previously failed standard IST did not respond to eltrombopag. No significant differences were observed in both cohorts with regard to infections. One IST-Epag-treated patient developed transient grade 3 transaminitis. Finally, no changes in paroxysmal nocturnal hemoglobinuria (PNH) clone size and cytogenetic abnormalities were seen in either cohort. The addition of eltrombopag to standard IST was well tolerated and resulted in satisfactory hematological response at 6 and 12 months in this single-institution experience. A larger cohort with longer follow-up is required to assess response durability.


Perforated Peptic Ulcer Disease in a Tertiary Hospital, Addis Ababa, Ethiopia: Five Year Retrospective Study.
Peptic ulcer perforation is one of the two major acute complications of peptic ulcer disease with significant morbidity and mortality. Institution based retrospective review was done to determine patient presentation, management and postoperative complications of perforated peptic ulcer disease (PPUD) at a tertiary hospital in Addis Ababa, Ethiopia. Patients operated on from January 2013 to December 2017 were included. Univalent analysis was used to determine the influence of patient and operative events on postoperative outcomes. Totally, 136 patients were studied. Males outnumbered females by a ratio of 5.5:1. The mean age of patients was 36.05±16.56 years. Seventy-one (52.2%) patients presented after twenty-four hours of onset of symptoms. Most perforations were located on the first part of the duodenum (117,86%). There were 73 postoperative complications recorded in 31(22.8%) patients. Old age, being female, presence of comorbidity, hypotension, tachycardia, and delayed presentation were significantly associated with postoperative morbidity (P<0.05). Nine (6.6%) patients died at the hospital. Mortality was significantly associated with old age, comorbid illness, tachycardia, and development of post-operative complications (P<0.05). The postoperative hospital stay of the patients with complications was 18.6 ± 14.7 days which was significantly higher than that of patients without complication 6.7±2.7days (P=0.001). Old age, being female, presence of comorbidity, hypotension, tachycardia, and delayed presentation were significantly associated with postoperative morbidity. Old age, comorbid illness, tachycardia and development of post-operative complications were found to increase the risk of mortality.


A Virtual Data Repository Stimulates Data Sharing in a Consortium.
Research data may have substantial impact beyond the original study objectives. The Collaborating Consortium of Cohorts Producing NIDA Opportunities (C3PNO) facilitates the combination of data and access to specimens from nine NIDA-funded cohorts in a virtual data repository (VDR). Unique challenges were addressed to create the VDR. An initial set of common data elements was agreed upon, selected based on their importance for a wide range of research proposals. Data were mapped to a common set of values. Bioethics consultations resulted in the development of various controls and procedures to protect against inadvertent disclosure of personally identifiable information. Standard operating procedures govern the evaluation of proposed concepts, and specimen and data use agreements ensure proper data handling and storage. Data from eight cohorts have been loaded into a relational database with tables capturing substance use, available specimens, and other participant data. A total of 6,177 participants were seen at a study visit within the past six months and are considered under active follow-up for C3PNO cohort participation as of the third data transfer, which occurred in January 2020. A total of 70,391 biospecimens of various types are available for these participants to test approved scientific hypotheses. Sociodemographic and clinical data accompany these samples. The VDR is a web-based interactive, searchable database available in the public domain, accessed at www.c3pno.org. The VDR are available to inform both consortium and external investigators interested in submitting concept sheets to address novel scientific questions to address high priority research on HIV/AIDS in the context of substance use.


Bioavailability and fate of sediment-associated trenbolone and estradiol in aquatic systems.
Endocrine disrupting effects in aquatic organisms have been observed in systems influenced by steroid hormones. Associating endocrine disruption with aqueous concentrations of steroids alone may overlook the influence of source-sink dynamics in sediments on steroid hormone bioavailability. The objective of this study was to determine the fate of 17β-estradiol and 17β-trenbolone in two field sediments and to evaluate the corresponding bioavailability of the compounds to the fathead minnow (Pimephales promelas). Steroid fate was evaluated using analytical chemistry and verified by assessing the biological activity using yeast based in vitro assays. Effective bioavailability of the steroids was inferred from changes in hepatic vitellogenin expression (increased expression in males exposed to 17β-estradiol, and reduced expression in females exposed to 17β-trenbolone). In experiments conducted with 17β-estradiol, no induction of hepatic vitellogenin mRNA expression was observed in male fish exposed to sediment-associated 17β-estradiol. In contrast, female minnows exposed to sediment-associated 17β-trenbolone experienced significant reductions in hepatic vitellogenin compared to negative controls. In both systems, the parent compounds were shown to degrade rapidly to the more persistent metabolites, estrone and trendione, both of which were found predominantly associated with the sediments. Results from the yeast estrogen screen indicate a reduction in biological activity as biotransformation of 17β-estradiol occurs; results from the yeast anti-estrogen screen were inconclusive and unable to substantiate 17β-trenbolone fate in aquatic systems. Collectively, these data support the contention that steroid hormones associated with the sediment can become bioavailable to fish, and that sediment characteristics influence the observed bioavailability of these compounds.


DermO; an ontology for the description of dermatologic disease.
There have been repeated initiatives to produce standard nosologies and terminologies for cutaneous disease, some dedicated to the domain and some part of bigger terminologies such as ICD-10. Recently, formally structured terminologies, ontologies, have been widely developed in many areas of biomedical research. Primarily, these address the aim of providing comprehensive working terminologies for domains of knowledge, but because of the knowledge contained in the relationships between terms they can also be used computationally for many purposes. We have developed an ontology of cutaneous disease, constructed manually by domain experts. With more than 3000 terms, DermO represents the most comprehensive formal dermatological disease terminology available. The disease entities are categorized in 20 upper level terms, which use a variety of features such as anatomical location, heritability, affected cell or tissue type, or etiology, as the features for classification, in line with professional practice and nosology in dermatology. Available in OBO flatfile and OWL 2 formats, it is integrated semantically with other ontologies and terminologies describing diseases and phenotypes. We demonstrate the application of DermO to text mining the biomedical literature and in the creation of a network describing the phenotypic relationships between cutaneous diseases. DermO is an ontology with broad coverage of the domain of dermatologic disease and we demonstrate here its utility for text mining and investigation of phenotypic relationships between dermatologic disorders. We envision that in the future it may be applied to the creation and mining of electronic health records, clinical training and basic research, as it supports automated inference and reasoning, and for the broader integration of skin disease information with that from other domains.


A novel thin NIPAM gel cassette dosimeter for photon-beam radiotherapy.
The response of thin polymer gel cassettes (called NIPAM gels) to ionizing radiation was investigated in this study. The NIPAM gels were prepared from gelatin, N-isopropyl acrylamide, tetrakis (hydroxymethyl) phosphoniumchloride, and N,N'-methylene-bis-acrylamide. Gel cassettes were irradiated in a phantom using a linear accelerator, and the polymerization morphology of irradiated NIPAM gel was characterized using scanning electron microscopy. The dose-response sensitivity of the NIPAM gels was evaluated using the differences in optical densities. The optical densities were obtained using a computer-controlled CCD camera that was connected to a planar illumination source for acquisition of optical transmission images. The central axis depth dose profiles of the phantom were extracted, and a comparison with ionization chamber measurements demonstrated similarities in profiles. The sensitivity, linearity of the response, accuracy, and reproducibility of the polymer gel cassettes were acceptable. However, the profiles of the half-blocked field irradiation showed no significant dispersion in the visible region. This study also extensively investigated the spatial stability of the NIPAM gel. The results showed that the gel cassette response remains stable for up to three months after irradiation.