Low sensitivity to alcohol: relations with hangover occurrence and susceptibility in an ecological momentary assessment investigation.
The current investigation tested whether low sensitivity to alcohol, as measured by the Self-Rating of the Effects of Alcohol (SRE) form, is associated with hangover occurrence or resistance, two potentially important predictors of later problematic drinking outcomes. Drinkers who reported using alcohol at least four times in the past month (N = 402) completed the SRE at baseline and used ecological momentary assessment methods with an electronic diary to record drinking behaviors and related experiences over 21 days. Each morning, the diary assessed prior-night drinking behaviors and the presence of current hangover. After adjustments for sex, body weight, age, and smoking status, higher SRE scores (indicating lower alcohol sensitivity) predicted hangover occurrence on postdrinking mornings (odds ratio [OR] = 1.24 per interquartile range [IQR], p = .003). However, when the number of drinks consumed in the drinking episode was covaried, SRE scores were negatively associated with hangover (OR = 0.67 per IQR, p <.001). An interaction between SRE scores and the number of drinks consumed indicated that low-sensitivity drinkers tend to be differentially resistant to hangover at a given number of drinks. Higher SRE scores were associated with consuming more drinks on average (generalized estimating equations coefficient = 2.20 per IQR, p <.001). Individuals lower in alcohol sensitivity appear to be more resistant to hangovers per unit of alcohol. However, they are also more likely to engage in excessive drinking, and this may account for their increased odds of experiencing hangover during an arbitrary monitoring period. Heavy consumption, hangover resistance, and hangover frequency may each be manifestations of low sensitivity to alcohol, an established risk factor for alcohol use disorder.


Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord.
The coordinated spatial and temporal regulation of gene expression in the vertebrate neural tube determines the identity of neural progenitors and the function and physiology of the neurons they generate. Progress has been made deciphering the gene regulatory programmes that are responsible for this process; however, the complexity of the tissue has hampered the systematic analysis of the network and the underlying mechanisms. To address this, we used single cell mRNA sequencing to profile cervical and thoracic regions of the developing mouse neural tube between embryonic days 9.5-13.5. We confirmed that the data accurately recapitulates neural tube development, allowing us to identify new markers for specific progenitor and neuronal populations. In addition, the analysis highlighted a previously underappreciated temporal component to the mechanisms that generate neuronal diversity, and revealed common features in the sequence of transcriptional events that lead to the differentiation of specific neuronal subtypes. Together, the data offer insight into the mechanisms that are responsible for neuronal specification and provide a compendium of gene expression for classifying spinal cord cell types that will support future studies of neural tube development, function and disease.


Analysis of nursing assessments in a cohort patients with ruptured cerebral aneurysms.
Patients admitted with subarachnoid hemorrhage are monitored for symptoms of vasospasm. A prospective study was designed to compare two monitoring instruments: a standard neurological tool (SNR) and the National Institutes of Health Stroke Scale (NIHSS). The two assessment tools were compared to evaluate their concordance and to identify areas where efficiency in recording assessments might be improved. We found no statistical difference between the two tools in detecting symptomatic cerebral vasospasm. Substantial discrepancies in the documentation of observations were noted, particularly in the assessment of limb drift. Avoidance of these discrepancies may require further definition in the SNR tool. A qualitative component consisting of a review of the nurses' notes regarding neurological status in the patients' charts was conducted. It was demonstrated that nurses commonly document information in the progress notes that is already captured in the SNR. Further education of nurses in the use of assessment tools is therefore recommended to avoid redundancies and increase efficiency in recording clinical observations.


Combinations of SNPs related to signal transduction in bipolar disorder.
Any given single nucleotide polymorphism (SNP) in a genome may have little or no functional impact. A biologically significant effect may possibly emerge only when a number of key SNP-related genotypes occur together in a single organism. Thus, in analysis of many SNPs in association studies of complex diseases, it may be useful to look at combinations of genotypes. Genes related to signal transmission, e.g., ion channel genes, may be of interest in this respect in the context of bipolar disorder. In the present study, we analysed 803 SNPs in 55 genes related to aspects of signal transmission and calculated all combinations of three genotypes from the 3×803 SNP genotypes for 1355 controls and 607 patients with bipolar disorder. Four clusters of patient-specific combinations were identified. Permutation tests indicated that some of these combinations might be related to bipolar disorder. The WTCCC bipolar dataset were use for replication, 469 of the 803 SNP were present in the WTCCC dataset either directly (n = 132) or by imputation (n = 337) covering 51 of our selected genes. We found three clusters of patient-specific 3×SNP combinations in the WTCCC dataset. Different SNPs were involved in the clusters in the two datasets. The present analyses of the combinations of SNP genotypes support a role for both genetic heterogeneity and interactions in the genetic architecture of bipolar disorder.


Idiopathic pulmonary fibrosis: update on genetic discoveries.
Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic disease of the lungs that increases in prevalence with advanced age. Recent evidence indicates that mutations in genes of two different biologic pathways lead to the common phenotype of familial pulmonary fibrosis (FPF) and sporadic IPF. Mutations in the genes encoding the lung surfactant proteins C and A2 (SFTPC and SFTPA2, respectively) cause increased endoplasmic reticulum stress in type II alveolar epithelial cells. Mutations in the genes encoding telomerase (TERT and TERC) cause IPF through shortening of telomere lengths and probable exhaustion of lung stem cells. All of the mutations are individually rare, but, collectively, TERT mutations are the most common genetic defect found in FPF. The overall penetrance of pulmonary fibrosis in TERT mutation carriers is 40% in subjects with a mean age of 51 years. Penetrance increases with advanced age, is greater in males than in females, and is positively associated with fibrogenic environmental exposures. Short telomere lengths are found in patients with FPF and sporadic IPF without mutations in telomerase, suggesting that the biologic pathway of telomerase dysfunction provides a biologic explanation for the age-related prevalence of IPF. The molecular data of two seemingly unrelated biologic pathways-alveolar epithelial endoplasmic reticulum stress and telomerase dysfunction-are beginning to elucidate the pathogenesis of IPF. These results have potentially predictive and therapeutic value.


Severe fatigue in patients with adrenal insufficiency: physical, psychosocial and endocrine determinants.
Fatigue is a frequently experienced complaint in patients with adrenal insufficiency (AI) and may be influenced by cortisol levels. The objective of this study was to determine the prevalence of severe fatigue in adrenal insufficiency (AI) patients, to assess which dimensions contribute to fatigue severity and to determine the association between salivary cortisol levels and momentary fatigue. We performed a cross-sectional study in the outpatient department of a university hospital. Included were 27 patients with congenital adrenal hyperplasia (CAH), 26 patients with primary AI (PAI), 24 patients with secondary AI (SAI) and 31 patients with adrenal insufficiency after treatment for Cushing's syndrome (Cush-AI). Measurements included computerised questionnaires to determine fatigue severity and physical and psychosocial contributors. Patients took four saliva samples at home, in which cortisol levels were measured. Severe fatigue was experienced by 41 % of the CAH patients, 42 % of the PAI patients, 50 % of the SAI patients and 42 % of the Cush-AI patients. Psychological distress, functional impairment, sleep disturbance, physical activity, concentration problems and social functioning contributed to the subjective experience of fatigue. Salivary cortisol levels were not correlated with momentary fatigue. A considerable proportion of AI patients experience severe fatigue. Salivary cortisol level is not a significant predictor for momentary fatigue in AI patients.


The chick somitogenesis oscillator is arrested before all paraxial mesoderm is segmented into somites.
Somitogenesis is the earliest sign of segmentation in the developing vertebrate embryo. This process starts very early, soon after gastrulation has initiated and proceeds in an anterior-to-posterior direction during body axis elongation. It is widely accepted that somitogenesis is controlled by a molecular oscillator with the same periodicity as somite formation. This periodic mechanism is repeated a specific number of times until the embryo acquires a defined specie-specific final number of somites at the end of the process of axis elongation. This final number of somites varies widely between vertebrate species. How termination of the process of somitogenesis is determined is still unknown. Here we show that during development there is an imbalance between the speed of somite formation and growth of the presomitic mesoderm (PSM)/tail bud. This decrease in the PSM size of the chick embryo is not due to an acceleration of the speed of somite formation because it remains constant until the last stages of somitogenesis, when it slows down. When the chick embryo reaches its final number of somites at stage HH 24-25 there is still some remaining unsegmented PSM in which expression of components of the somitogenesis oscillator is no longer dynamic. Finally, we identify a change in expression of retinoic acid regulating factors in the tail bud at late stages of somitogenesis, such that in the chick embryo there is a pronounced onset of Raldh2 expression while in the mouse embryo the expression of the RA inhibitor Cyp26A1 is downregulated. Our results show that the chick somitogenesis oscillator is arrested before all paraxial mesoderm is segmented into somites. In addition, endogenous retinoic acid is probably also involved in the termination of the process of segmentation, and in tail growth in general.


Multi-institutional Comparison of Temporal Bone Models: A Collaboration of the AAO-HNSF 3D-Printed Temporal Bone Working Group.
The American Academy of Otolaryngology-Head and Neck Surgery Foundation's (AAO-HNSF's) 3D-Printed Temporal Bone Working Group was formed with the goal of sharing information and experience relating to the development of 3D-printed temporal bone models. The group conducted a multi-institutional study to directly compare several recently developed models. Expert opinion survey. Temporal bone laboratory. The working group convened in 2018. The various methods in which 3D virtual models had been created and printed in physical form were then shared and recorded. This allowed for comparison of the advantages, disadvantages, and costs of each method. In addition, a drilling event was held during the October 2018 AAO-HNSF Annual Meeting. Each model was drilled and evaluated by attending-level working group members using an 15-question Likert scale questionnaire. The models were graded on anatomic accuracy as well as their suitability as a simulation of both cadaveric and operative temporal bone drilling. The models produced for this study demonstrate significant anatomic detail and a likeness to human cadaver specimens for drilling and dissection. Models printed in standard resin material with a stereolithography printer scored highest in the evaluation, though the margin of difference was negligible in several categories. Simulated 3D temporal bones created through a number of printing methods have potential benefit in surgical training, preoperative simulation for challenging otologic cases, and the standardized testing of temporal bone surgical skills.


Urolithiasis in renal transplantation: diagnosis and management.
To report our experience of diagnosis and multimodal management of urolithiasis in renal transplantation. From January 1995 to December 2012, 953 patients underwent renal transplantation in the Kidney Transplant Unit of Treviso General Hospital. Ten (10%) of them developed urinary calculi and were referred at our institution. Their mode of presentation, investigation and treatment were recorded. Seven had renal and 3 ureteral calculi. Urolithiasis was incidentally discovered on routine ultrasound in 6 patients, 1 presented with oliguria, 1 with anuria and acute renal failure and in 2 urolithiasis was found at removal of the ureteral stent. Nephrostomy tube was placed in 5 patients. Hypercalcemia with hyperparathyroidism (HPT) was present in 5 patients and hyperuricemia in 3. Two patients were primary treated by shock wave lithotripsy (SWL) and one of them was stone-free after two sessions. Two patients, one with multiple pielocaliceal calculi and the other with staghorn calculus in the lower calyx, were treated with percutaneous nephrolitothotomy (PCNL). Three patients were treated by ureteroscopy (URS) and in one of them two treatments were carried out. One patient had calculus impacted in the uretero-vesical anastomosis and surgical ureterolithotomy with re-do ureterocystoneostomy was performed after failure of URS. Two patients with calculi discovered at removal of the ureteral stent were treated by URS. The incidence of urolithiasis in renal transplantation is uncommon. In the most of patients the condition occurs without pain. Metabolic anomalies and medical treatment after renal transplantation may cause stone formation. Advancements in endourology and interventional radiology have influenced the management of urolithiasis that can be actually treated with a minimal incidence of risk for the renal allograft.


Biotic homogenization within and across eight widely distributed grasslands following invasion by Bromus inermis.
Invasive species can alter the structure and function of the communities they invade, as well as lead to biotic homogenization across their invasive range, thus affecting large-scale diversity patterns. The mechanisms by which invasive species can lead to biotic homogenization are poorly understood. We argue that invasive species acting as strong, deterministic, and consistent filters within and across invaded communities are likely to cause biotic homogenization at multiple spatial scales. We studied Bromus inermis Leyss. invasion into eight grasslands covering most of the grassland and parkland natural regions of Alberta (western Canada). Specifically, we tested whether B. inermis (1) has a strong impact on species richness and composition, (2) consistently alters resources (nutrients, light, and soil moisture), imposing the same ecological filter to species establishment and persistence across sites, and hence (3) whether it leads to biotic homogenization within and across sites. We recorded plant cover and resources across native-to-invaded transition areas combining space-for-time substitutions with time-series data analyses. Bromus inermis invasion was associated with rapid biotic homogenization of communities, within and among the eight grasslands. The sharp changes in species relative abundances following invasion was the initial driver of biotic homogenization, and species loss was delayed. Supporting the idea that biotic homogenization can occur when an invasive species presents a broad and consistent filter, resources modified by B. inermis invasion (particularly light and certain nutrients) were altered rather consistently within and across sites. The 50% reduction in light was likely the initial driver of biotic homogenization, and the increase in nutrient availability probably facilitates the displacement of species from the invaded areas and could lead to the establishment of self-reinforcing dynamics. Overall, our results support the idea that invaders acting as strong, deterministic, and consistent ecological filters are likely to cause biotic homogenization of the communities they invade.


In Situ Preparation of Metal Halide Perovskite Nanocrystal Thin Films for Improved Light-Emitting Devices.
Hybrid organic-inorganic halide perovskite semiconductors are attractive candidates for optoelectronic applications, such as photovoltaics, light-emitting diodes, and lasers. Perovskite nanocrystals are of particular interest, where electrons and holes can be confined spatially, promoting radiative recombination. However, nanocrystalline films based on traditional colloidal nanocrystal synthesis strategies suffer from the use of long insulating ligands, low colloidal nanocrystal concentration, and significant aggregation during film formation. Here, we demonstrate a facile method for preparing perovskite nanocrystal films in situ and that the electroluminescence of light-emitting devices can be enhanced up to 40-fold through this nanocrystal film formation strategy. Briefly, the method involves the use of bulky organoammonium halides as additives to confine crystal growth of perovskites during film formation, achieving CH3NH3PbI3 and CH3NH3PbBr3 perovskite nanocrystals with an average crystal size of 5.4 ± 0.8 nm and 6.4 ± 1.3 nm, respectively, as confirmed through transmission electron microscopy measurements. Additive-confined perovskite nanocrystals show significantly improved photoluminescence quantum yield and decay lifetime. Finally, we demonstrate highly efficient CH3NH3PbI3 red/near-infrared LEDs and CH3NH3PbBr3 green LEDs based on this strategy, achieving an external quantum efficiency of 7.9% and 7.0%, respectively, which represent a 40-fold and 23-fold improvement over control devices fabricated without the additives.


DNA polymerases that propagate the eukaryotic DNA replication fork.
Three DNA polymerases are thought to function at the eukaryotic DNA replication fork. Currently, a coherent model has been derived for the composition and activities of the lagging strand machinery. RNA-DNA primers are initiated by DNA polymerase ot-primase. Loading of the proliferating cell nuclear antigen, PCNA, dissociates DNA polymerase ca and recruits DNA polymerase S and the flap endonuclease FEN1 for elongation and in preparation for its requirement during maturation, respectively. Nick translation by the strand displacement action of DNA polymerase 8, coupled with the nuclease action of FEN1, results in processive RNA degradation until a proper DNA nick is reached for closure by DNA ligase I. In the event of excessive strand displacement synthesis, other factors, such as the Dna2 nuclease/helicase, are required to trim excess flaps. Paradoxically, the composition and activity of the much simpler leading strand machinery has not been clearly established. The burden of evidence suggests that DNA polymerase E normally replicates this strand,but under conditions of dysfunction, DNA polymerase 8 may substitute.


Effect of oral treatment of Perilla frutescens and its constituents on type-I allergy in mice.
Perilla frutescens Britton (perilla, Labiatae) is a medicinal herb prescribed in Saiboku-to [Japanese letters: see text], which is a Kampo formula effective for allergic diseases such as bronchial asthma. The present study was conducted to evaluate the anti-allergic effect of orally administered perilla decoction and to identify the active constituents using mice ear-passive cutaneous anaphylaxis (PCA)-reaction, which is one of the animal models for type I allergy. Perilla decoction significantly suppressed PCA-reaction, and the inhibition % at the dose of 500 mg/kg was 43%. The perilla decoction contains 5.3% of luteolin 7-O-[beta-glucuronosyl(2-->1)beta-glucuronide], 1.6% of apigenin 7-O-[beta-glucuronosyl(2-->1)beta-glucuronide], 0.49% of scutellarin, and 2.5% of rosmarinic acid (weight of compound/dried weight of perilla decoction %), respectively. When these constituents were orally administered to mice at the dose equivalent to 500 mg/kg of perilla decoction, rosmarinic acid and apigenin 7-O-[beta-glucuronosyl(2-->1)beta-glucuronide] significantly suppressed PCA-reaction, and their inhibition % was 41% (p<0.01) and 32% (p<0.05), respectively. Since the inhibition % or perilla decoction and rosmarinic acid were nearly equal, the anti-allergic effect of perilla decoction depends primarily on rosmarinic acid. The standard Saiboku-to decoction contained 0.013% of rosmarinic acid, which was too low to exhibit anti-allergic activity in a daily dose of Saiboku-to in adults, suggesting that perilla would be prescribed in Saiboku-to to exhibit other pharmacological effects than its anti-allergic activity, such as a sedative.


An interleukin 1 like factor stimulates bone resorption in vitro.
Many activities are now ascribed to the monokine interleukin 1 including enhancement of immune responses, stimulation of thymocyte proliferation, activation of B cells, stimulation of proteinase and prostaglandin production by connective tissue cells, stimulation of the production of acute phase proteins, induction of fever and the induction of neutrophilia. These activities were thought to be due to various different factors, but are now considered probably due to very similar, if not identical, molecules. The term interleukin 1 (IL-1) was coined to describe the factor released by monocyte/macrophages which acts on T and B lymphocytes. Only after this definition had been accepted was it shown that target cells other than lymphocytes were affected by IL-1. Products of human blood monocytes (mononuclear cell factor, MCF) have been implicated in the pathogenesis of inflammatory diseases such as rheumatoid arthritis and periodontal disease. Bone resorption is often a feature of such diseases, and monocytes are frequently found at sites of localized bone resorption. Preliminary experiments with monocyte-conditioned medium indicated that MCF could stimulate bone resorption. We therefore undertook this study to verify these observations and to determine whether purified IL-1 could stimulate connective tissue breakdown in vitro.


Epoxyeicosatrienoic acids: a double-edged sword in cardiovascular diseases and cancer.
Epoxyeicosatrienoic acids (EETs) generated from arachidonic acid by cytochrome P450 (CYP) epoxygenases have beneficial effects in certain cardiovascular and kidney diseases. Hence, great efforts have been made to develop drugs targeting the EET pathway. Some of these agents are currently under evaluation in clinical trials for treatment of hypertension and diabetes. In this issue of the JCI, Panigrahy et al. evaluate in a systematic way the role of CYP epoxygenases and the metabolites they generate in cancer progression. Their findings, along with previous studies, raise concerns about using these drugs in humans.


Gold nanoconjugates reinforce the potency of conjugated cisplatin and doxorubicin.
Osteosarcoma or osteogenic sarcoma is the most common and prevalent cancerous tumor of bone and occurs especially in children and teens. Recent treatment strategy includes a combination of both chemotherapy and surgeries. Although, the use of single drug-based chemotherapy treatment remains unsatisfactory. Therefore, combinatorial therapy has emerged as a potential strategy for treatment with limited side- effects. Here, we evaluated the combinatorial anticancerous effect of cisplatin (CIS) and doxorubicin (DOX) bioconjugated bromelain encapsulated gold nanoparticles (B-AuNPs conjugated CIS and DOX) in the treatment of osteosarcoma. The synthesized B-AuNPs conjugated CIS and DOX were characterized by various characterization techniques like UV-vis spectroscopy, TEM, DLS and zeta potential to ensure the synthesis, size, shape, size distribution and stability. Drug loading efficiency bioconjugation of CIS and DOX was ensured by UV-vis spectroscopy. Bioconjugation of CIS and DOX was further confirmed using UV-vis spectroscopy, TEM, DLS, Zeta potential and FT-IR analysis. The combinatorial effect of CIS and DOX in B-AuNPs conjugated CIS and DOX showed highly improved potency against MG-63 and Saos-2 cells at a very low concentration where primary osteoblasts didn't show any cytotoxic effect. The apoptotic effect of B-AuNPs conjugated CIS and DOX on osteosarcoma and primary osteoblasts cells were analyzed by increased permeability of the cell membrane, condensed chromatin and deep blue fluorescent condensed nucleus. The results clearly showed that B-AuNPs conjugated CIS and DOX significantly improved the potency of both the chemotherapeutic drugs by delivering them specifically into the nucleus of cancer cells through caveolae-dependent endocytosis. Thus, the greater inhibitory effect of combinatorial drugs (B-AuNPs conjugated CIS and DOX) over single drug based chemotherapy would be of great advantage during osteosarcoma treatment.


A robust computational framework for estimating 3D Bi-Atrial chamber wall thickness.
Atrial fibrillation (AF) is the most prevalent form of cardiac arrhythmia. The atrial wall thickness (AWT) can potentially improve our understanding of the mechanism underlying atrial structure that drives AF and provides important clinical information. However, most existing studies for estimating AWT rely on ruler-based measurements performed on only a few selected locations in 2D or 3D using digital calipers. Only a few studies have developed automatic approaches to estimate the AWT in the left atrium, and there are currently no methods to robustly estimate the AWT of both atrial chambers. Therefore, we have developed a computational pipeline to automatically calculate the 3D AWT across bi-atrial chambers and extensively validated our pipeline on both ex vivo and in vivo human atria data. The atrial geometry was first obtained by segmenting the atrial wall from the MRIs using a novel machine learning approach. The epicardial and endocardial surfaces were then separated using a multi-planar convex hull approach to define boundary conditions, from which, a Laplace equation was solved numerically to automatically separate bi-atrial chambers. To robustly estimate the AWT in each atrial chamber, coupled partial differential equations by coupling the Laplace solution with two surface trajectory functions were formulated and solved. Our pipeline enabled the reconstruction and visualization of the 3D AWT for bi-atrial chambers with a relative error of 8% and outperformed existing algorithms by >7%. Our approach can potentially lead to improved clinical diagnosis, patient stratification, and clinical guidance during ablation treatment for patients with AF.


Infection enhancement of dengue type 2 virus in the U-937 human monocyte cell line by antibodies to flavivirus cross-reactive determinants.
Dengue type 2 virus replication was detected in the U-937 human monocyte cell line when the virus inoculum and the culture medium contained flavivirus antibodies diluted beyond their neutralizing titers. This was in marked contrast to yellow fever virus, which replicated very well in the absence of antibodies; however, 10-fold-higher yields of yellow fever virus could be obtained in the presence of flavivirus antibodies. These infection-enhancing antibodies were obtained from either a dengue type 2 human antiserum or reference hyperimmune obtained from either a dengue type 2 human antiserum or reference hyperimmune mouse ascitic fluid. The infection enhancement phenomenon, previously shown to be due to infection of Fc receptor-bearing cells with virus-antibody complexes, was completely blocked by preincubation of the cells with aggregated gamma globulin. The blocking results suggested an Fc receptor-mediated infection of the U-937 cells as well. A panel of monoclonal antibodies, previously characterized as either virus type specific or flavivirus cross-reactive and with mouse immunoglobulin subclasses G1 and G2a in both categories, were tested for their infection enhancement characteristics. A type-specific neutralizing monoclonal antibody preparation that was diluted beyond its neutralization titer did not cause infection enhancement, nor did low-level neutralizing monoclonal antibodies that were dengue serotype specific by the hemagglutination inhibition test. Only flavivirus cross-reactive monoclonal antibodies caused infection enhancement, irrespective of whether the immunoglobulins were G1 or G2a. These cross-reactive flavivirus determinants may reside at the tips of the glycoprotein projections on the virus particles, enabling the Fc ends of the cross-reactive antibodies attached to these determinants to interact with Fc receptors on susceptible cells.


Selecting potential children and unconditional parental love.
For now, the best way to select a child's genes is to select a potential child who has those genes, using genetic testing and either selective abortion, sperm and egg donors, or selecting embryos for implantation. Some people even wish to select against genes that are only mildly undesirable, or to select for superior genes. I call this selection drift--the standard for acceptable children is creeping upwards. The President's Council on Bioethics and others have raised the parental love objection: Just as we should love existing children unconditionally, so we should unconditionally accept whatever child we get in the natural course of things. If we set conditions on which child we get, we are setting conditions on our love for whatever child we get. Although this objection was prompted by selection drift, it also seems to cover selecting against genes for severe impairments. I argue that selection drift is not inconsistent with the ideal of unconditional parental love and, moreover, that the latter actually implies that we should practise selection drift--in other words, we should try to select potential children with the best genetic endowments. My endowment argument for the second claim works from an analogy between arranging an endowment prior to conception to fund a future child's education, and arranging a genetic endowment by selecting a potential child who already has it, where in both cases the child would not have existed without the endowment. I conclude with some programmatic remarks about the nonidentity problem.


Cinacalcet use in paediatric dialysis: a position statement from the European Society for Paediatric Nephrology and the Chronic Kidney Disease-Mineral and Bone Disorders Working Group of the ERA-EDTA.
Secondary hyperparathyroidism (SHPT) is an important complication of advanced chronic kidney disease (CKD) in children, which is often difficult to treat with conventional therapy. The calcimimetic cinacalcet is an allosteric modulator of the calcium-sensing receptor. It has proven to be effective and safe in adults to suppress parathyroid hormone (PTH), but data on its use in children are limited. To date, studies in children only consist of two randomized controlled trials, nine uncontrolled interventional or observational studies, and case reports that report the efficacy of cinacalcet as a PTH-lowering compound. In 2017, the European Medical Agency approved the use of cinacalcet for the treatment of SHPT in children on dialysis in whom SHPT is not adequately controlled with standard therapy. Since evidence-based guidelines are so far lacking, we present a position statement on the use of cinacalcet in paediatric dialysis patients based on the available evidence and opinion of experts from the European Society for Paediatric Nephrology, Chronic Kidney Disease-Mineral and Bone Disorder and Dialysis Working Groups, and the ERA-EDTA. Given the limited available evidence the strength of these statements are weak to moderate, and must be carefully considered by the treating physician and adapted to individual patient needs as appropriate. Audit and research recommendations to study key outcome measures in paediatric dialysis patients receiving cinacalcet are suggested.


[Causes of acute poisoning with medication in a southern Brazilian city].
Acute poisoning with medicines in Brazil has various causes, including a deficient national drug policy. The current study thus aimed to analyze socioeconomic variables, prescription characteristics, and forms of purchase or acquisition and storing of medicines by victims of acute unintentional poisoning. The data were collected during home visits to patients with a record of acute unintentional drug poisoning according to the Poison Control Center in Maringá, Paraná State, in 2004. The variables were related to the victim, the poisoning event, the product, and its household storage. For the 97 poisonings recorded during the study period, 72 families were interviewed, with the majority of the victims under 10 years of age (73.6%), males (54.2%), and from lower-income groups (63.9%). Many interviewees reported not having received information about the drug (76.5%). There was a significant association between lower-income status and inadequate drug storage (p < 0.05). A larger proportion of poisonings in higher-income families involved expired products (p < 0.05). Inadequate acquisition and storage of drugs may thus have facilitated the occurrence of poisonings.


ER71 directs mesodermal fate decisions during embryogenesis.
Er71 mutant embryos are nonviable and lack hematopoietic and endothelial lineages. To further define the functional role for ER71 in cell lineage decisions, we generated genetically modified mouse models. We engineered an Er71-EYFP transgenic mouse model by fusing the 3.9 kb Er71 promoter to the EYFP reporter gene. Using FACS and transcriptional profiling, we examined the EYFP(+) population of cells in Er71 mutant and wild-type littermates. In the absence of ER71, we observed an increase in the number of EYFP-expressing cells, increased expression of the cardiac molecular program and decreased expression of the hemato-endothelial program, as compared with wild-type littermate controls. We also generated a novel Er71-Cre transgenic mouse model using the same 3.9 kb Er71 promoter. Genetic fate-mapping studies revealed that the ER71-expressing cells give rise to the hematopoietic and endothelial lineages in the wild-type background. In the absence of ER71, these cell populations contributed to alternative mesodermal lineages, including the cardiac lineage. To extend these analyses, we used an inducible embryonic stem/embryoid body system and observed that ER71 overexpression repressed cardiogenesis. Together, these studies identify ER71 as a critical regulator of mesodermal fate decisions that acts to specify the hematopoietic and endothelial lineages at the expense of cardiac lineages. This enhances our understanding of the mechanisms that govern mesodermal fate decisions early during embryogenesis.


The expression pattern of a novel gene encoding brain-fatty acid binding protein correlates with neuronal and glial cell development.
Fatty acid binding proteins (FABPs) are a multigene family of small intracellular proteins that bind hydrophobic ligands. In this report we describe the cloning and expression pattern of a novel member of this gene family that is specifically expressed in the developing and adult nervous system and thus was designated brain (B)-FABP. B-FABP is closely related to heart (H)-FABP with 67% amino acid identity. B-FABP expression was first detected at mouse embryonic day 10 in neuroepithelial cells and its pattern correlates with early neuronal differentiation. Upon further development, B-FABP was confined to radial glial cells and immature astrocytes. B-FABP mRNA and protein were found in glial cells of the peripheral nervous system such as satellite cells of spinal and cranial ganglia and ensheathing cells of the olfactory nerve layer from as early as embryonic day 11 until adulthood. In the adult mouse brain, B-FABP was found in the glia limitans, in radial glial cells of the hippocampal dentate gyrus and Bergman glial cells. These findings suggest a function of B-FABP during neurogenesis or neuronal migration in the developing nervous system. The partially overlapping expression pattern with that of cellular retinoid binding proteins suggests that B-FABP is involved in the metabolism of a so far unknown hydrophobic ligand with potential morphogenic activity during CNS development.


Evidence for at least two major loci influencing human fatness.
The genetics of human fatness has been the subject of many recent studies, motivated by the increased morbidity and mortality associated with obesity, as well as the increasing prevalence of overweight and obesity. The body-mass index (BMI) and fat mass (FM), measured by underwater weighing, were assessed for 1,630 individuals from approximately 300 families from phase 1 of the Quebec Family Study. The two phenotypes are highly correlated ( approximately .8) in adults, and previous segregation analysis revealed evidence for a recessive major gene for each trait. In our study, we utilized bivariate segregation analysis to determine the source(s) of phenotypic correlation-namely, a pleiotropic major gene, shared familial factors/polygenes, or shared nontransmitted environmental factors. Analysis was performed by use of the Pedigree Analysis Package, with extensions to the bivariate case. Tests of hypotheses provided evidence for two pleiotropic recessive loci, together accounting for 64% and 47% of the variance in BMI and FM, respectively. Under the model, all sources of phenotypic correlation were significant: 73% of the covariance was attributed to the pleiotropic major loci, 8% to residual familial effects, and 19% to nontransmitted environmental factors. The high degree of genetic identity between the two traits is not surprising, since the BMI often is used as a surrogate for FM; however, simultaneous analysis of both phenotypes enabled the detection of a second major locus, which apparently does not affect extreme overweight (as does the primary major locus) but which affects variation in the "normal" range.


Solid-State 27Al NMR Spectroscopy of the γ-Al13 Keggin Containing Al Coordinated by a Terminal Hydroxyl Ligand.
We report solid-state 27Al NMR spectroscopic results for the sulfate salt of the γ-Al13 Keggin cluster, γ-[AlO4Al12(OH)25(OH2)11][SO4]3·[H2O]14, that provide a spectroscopic signature for partial hydrolysis of this Keggin-type cluster. In 27Al multiple-quantum magic-angle spinning NMR spectra, all 13 Al positions of the cluster are at least partially resolved and assigned with the aid of density functional theory (DFT) calculations of the 27Al electric field gradients. The isotropic chemical shift of the single tetrahedral site, 75.7 ppm, is nearly identical to that reported for solutions from which the cluster crystallizes. Reflecting broadly similar coordination environments, the octahedral Al show mostly small variations in isotropic chemical shift (+7 to +11 ppm) and quadrupolar coupling constant (CQ; 6-7.5 MHz), except for one resonance that exhibits a much smaller CQ and another site with a larger value. DFT calculations show that deprotonation of a terminal water ligand, to form an η-OH group, causes a large reduction in the 27Al CQ, allowing assignment of a distinct, narrow peak for octahedral Al to this hydroxyl-terminated site. This result suggests a relationship between octahedral 27Al NMR line width and hydrolysis for solids prepared from Keggin-type clusters.


An e-Chart Review of Chaplains' Interventions and Outcomes: A Quality Improvement and Documentation Practice Enhancement Project.
In Canada, the spiritual care landscape in health care settings is becoming more regulated and standardized documentation is part of this rigorous environment. Staff chaplains at The Ottawa Hospital participated in a Quality Improvement project that aimed to advance patient-centered care through better charting practices. A sample of 104 spiritual-care assessments that had been posted on the patient electronic health record was examined. This chart review focused on chaplains' activities that were reported as interventions as well as chaplain-reported outcomes for the patient. These interventions and outcomes were coded into discreet categories in order to get a better sense of the activities and the impact of their work. The chaplains' electronic charting content and practices were evaluated. Chaplains found that the Quality Improvement process was beneficial as they updated their electronic templates in order to meet the new reporting requirements of the College of Registered Psychotherapists of Ontario.


Variation in potassium transport properties of mouse 3T3 cells as a result of subcultivation.
Unindirectional potassium influx and the fraction of this influx sensitive to ouabain, an inhibitor of the (Na + K) activated ATPase, have been evaluated as a function of subcultivation of the 3T3 and SV40 transformed 3T3 cell. Total and ouabain-sensitive K influx change little over approximately 50 passages of the transformed 3T3 cell. In contrast, these components of K influx increase nearly 5-fold over a similar number of passages of the 3T3 cell. During early passages total and ouabain-sensitive K influx of the 3T3 cell are below that of the SV40 3T3 cell on a per cell volume basis. At later passages the magnitude of these components of K transport exceed those found in the SV40 3T3 cell. Previous studies have reported the ouabain-sensitive uptake of K and the levels of (Na + K) activated ATPase as being higher, lower or equivalent in the 3T3 versus transformed 3T3 cell. The present data suggest these differences may results from the degree to which the cells were passaged at the time of the experiments. Evaluation of previous studies substantiates this conclusion.


A computational model for periodic pattern perception based on frieze and wallpaper groups.
We present a computational model for periodic pattern perception based on the mathematical theory of crystallographic groups. In each N-dimensional Euclidean space, a finite number of symmetry groups can characterize the structures of an infinite variety of periodic patterns. In 2D space, there are seven frieze groups describing monochrome patterns that repeat along one direction and 17 wallpaper groups for patterns that repeat along two linearly independent directions to tile the plane. We develop a set of computer algorithms that "understand" a given periodic pattern by automatically finding its underlying lattice, identifying its symmetry group, and extracting its representative motifs. We also extend this computational model for near-periodic patterns using geometric AIC. Applications of such a computational model include pattern indexing, texture synthesis, image compression, and gait analysis.


Characterisation of avian pathogenic Escherichia coli (APEC) associated with colisepticaemia compared to faecal isolates from healthy birds.
A total of 114 avian pathogenic Escherichia coli (APEC) isolates were collected from cases of colisepticaemia occurring in broilers (77) and layers (37) within Ireland. In addition 45 strains isolated from faeces of healthy birds were included for comparison. All isolates were serogrouped, and examined for known virulence factors, mostly by PCR. The O78 serogroup represented 55 and 27% of broiler and layer colisepticaemic isolates respectively. All isolates were positive for curli fimbriae (crl, csg) and negative for afimbrial adhesin (afa). S-fimbrial (sfa) sequences were present in 8.8% of septicaemic isolates and 8.9% of healthy bird isolates. The majority of E. coli from cases of colisepticaemia (97.4%) and healthy bird (95.6%) isolates were positive for aerobactin (aer), and temperature sensitive haemagglutinin (tsh) was similarly detected in high numbers in 93.9 and 93.3%, respectively. In comparison to E. coli isolates from the faeces of healthy birds, a significantly higher percentage of isolates from septicaemic cases possessed Type 1 fimbriae (fimC) and increased serum survival (iss) gene sequences. Forty-seven (41.2%) isolates from septicaemic birds possessed P-fimbriae (pap) gene sequences, compared with only 15.6% from E. coli isolated from healthy birds. Haemolysin (hlyE) sequences were detected in 46.7% of isolates from healthy birds in comparison with 6.1% of septicaemic isolates. Sequences encoding colicin V (cvaC) were detected in 99.1% of septicaemic isolates and 82.2% of isolates from healthy birds. The K1 capsule was only present in two septicaemic isolates, both taken from layers. Motility was detected in 36.8% of E. coli isolated from cases of septicaemia, compared with 93.3% of isolates from healthy birds. These results demonstrate the presence of 11 virulence genes in E. coli isolated from cases of colisepticaemia within Ireland, and indicate the prevalence of iss and fimC.


Imine Hydrogels with Tunable Degradability for Tissue Engineering.
A shortage of available organ donors has created a need for engineered tissues. In this context, polymer-based hydrogels that break down inside the body are often used as constructs for growth factors and cells. Herein, we report imine cross-linked gels where degradation is controllable by the introduction of mixed imine cross-links. Specifically, hydrazide-functionalized poly(ethylene glycol) (PEG) reacts with aldehyde-functionalized PEG (PEG-CHO) to form hydrazone linked hydrogels that degrade quickly in media. The time to degradation can be controlled by changing the structure of the hydrazide group or by introducing hydroxylamines to form nonreversible oxime linkages. Hydrogels containing adipohydrazide-functionalized PEG (PEG-ADH) and PEG-CHO were found to degrade more rapidly than gels formed from carbodihydrazide-functionalized PEG (PEG-CDH). Incorporating oxime linkages via aminooxy-functionalized PEG (PEG-AO) into the hydrazone cross-linked gels further stabilized the hydrogels. This imine cross-linking approach should be useful for modulating the degradation characteristics of 3D cell culture supports for controlled cell release.


Adenoviral vector-mediated gene transfer and neurotransplantation: possibilities and limitations in grafting of the fetal rat suprachiasmatic nucleus.
Several studies have reported on the use of primary neural cells transduced by adenoviral vectors as donor cells in neurotransplantation. In the present investigation, we examined whether adenoviral vector-mediated gene transfer could be used to introduce and express a foreign gene in solid neural transplants of fetal suprachiasmatic nucleus (SCN) tissue. A recombinant adenoviral vector containing the reporter gene LacZ encoding for beta-galactosidase (Ad-LacZ) was used in order to establish the optimal procedure for ex vivo gene transfer. Expression of beta-galactosidase was dependent on the duration of the infection and on the vector concentration. Infection for a short period (< 4 h) with a high concentration of Ad-LacZ (3.4 x 10(9) pfu/ml), or for 18 h with a lower vector concentration (2 x 10(8) pfu/ml), resulted in expression of beta-galactosidase in a large number of neurons and glial cells up to 21 days in vitro. When infected fetal SCN tissue was implanted in the third ventricle of adult Wistar rats, expression was high after 8 days. After 21 days, the number of beta-galactosidase expressing cells had clearly declined, but expression remained present for at least 70 days. The method described in this paper might be applicable to introduce trophic factor genes in SCN grafts in order to support graft survival and to stimulate neurite outgrowth.


A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1.
The mechanism of substrate hydrolysis of New Delhi metallo-β-lactamase 1 (NDM-1) has been reported, but the process in which NDM-1 captures and transports the substrate into its active center remains unknown. In this study, we investigated the process of the substrate entry into the NDM-1 activity center through long unguided molecular dynamics simulations using meropenem as the substrate. A total of 550 individual simulations were performed, each of which for 200 ns, and 110 of them showed enzyme-substrate binding events. The results reveal three categories of relatively persistent and noteworthy enzyme-substrate binding configurations, which we call configurations A, B, and C. We performed binding free energy calculations of the enzyme-substrate complexes of different configurations using the molecular mechanics Poisson-Boltzmann surface area method. The role of each residue of the active site in binding the substrate was investigated using energy decomposition analysis. The simulated trajectories provide a continuous atomic-level view of the entire binding process, revealing potentially valuable regions where the enzyme and the substrate interact persistently and five possible pathways of the substrate entering into the active center, which were validated using well-tempered metadynamics. These findings provide important insights into the binding mechanism of meropenem to NDM-1, which may provide new prospects for the design of novel metallo-β-lactamase inhibitors and enzyme-resistant antibiotics.


Cellular oscillators: rhythmic gene expression and metabolism.
Many biological processes are driven by biological clocks that, depending on the frequency they generate, are classified into ultradian, circadian and infradian oscillators. In virtually all light-sensitive organisms from cyanobacteria to humans, a circadian timing system adapts cyclic physiology to geophysical time. Recent evidence suggests that even in mammals circadian oscillators function in a cell-autonomous manner. In yeast, an ultradian oscillator regulates cyclic respiratory activity and global gene expression. Circadian oscillators and the ultradian yeast respiratory clock share at least four properties: they follow limit-cycle kinetics, interweave with cellular metabolism, are temperature-compensated and influence the cell division clock.


A randomized pilot study comparing zero-calorie alternate-day fasting to daily caloric restriction in adults with obesity.
To evaluate the safety and tolerability of alternate-day fasting (ADF) and to compare changes in weight, body composition, lipids, and insulin sensitivity index (Si) with those produced by a standard weight loss diet, moderate daily caloric restriction (CR). Adults with obesity (BMI ≥30 kg/m(2) , age 18-55) were randomized to either zero-calorie ADF (n = 14) or CR (-400 kcal/day, n = 12) for 8 weeks. Outcomes were measured at the end of the 8-week intervention and after 24 weeks of unsupervised follow-up. No adverse effects were attributed to ADF, and 93% completed the 8-week ADF protocol. At 8 weeks, ADF achieved a 376 kcal/day greater energy deficit; however, there were no significant between-group differences in change in weight (mean ± SE; ADF -8.2 ± 0.9 kg, CR -7.1 ± 1.0 kg), body composition, lipids, or Si. After 24 weeks of unsupervised follow-up, there were no significant differences in weight regain; however, changes from baseline in % fat mass and lean mass were more favorable in ADF. ADF is a safe and tolerable approach to weight loss. ADF produced similar changes in weight, body composition, lipids, and Si at 8 weeks and did not appear to increase risk for weight regain 24 weeks after completing the intervention.


Assessment of effectiveness of percutaneous adhesiolysis in managing chronic low back pain secondary to lumbar central spinal canal stenosis.
Chronic persistent low back and lower extremity pain secondary to central spinal stenosis is common and disabling. Lumbar surgical interventions with decompression or fusion are most commonly performed to manage severe spinal stenosis. However, epidural injections are also frequently performed in managing central spinal stenosis. After failure of epidural steroid injections, the next sequential step is percutaneous adhesiolysis and hypertonic saline neurolysis with a targeted delivery. The literature on the effectiveness of percutaneous adhesiolysis in managing central spinal stenosis after failure of epidural injections has not been widely studied. A prospective evaluation. An interventional pain management practice, a specialty referral center, a private practice setting in the United States. To evaluate the effectiveness of percutaneous epidural adhesiolysis in patients with chronic low back and lower extremity pain with lumbar central spinal stenosis. Seventy patients were recruited. The initial phase of the study was randomized, double-blind with a comparison of percutaneous adhesiolysis with caudal epidural injections. The 25 patients from the adhesiolysis group continued with follow-up, along with 45 additional patients, leading to a total of 70 patients. All patients received percutaneous adhesiolysis and appropriate placement of the Racz catheter, followed by an injection of 5 mL of 2% preservative-free lidocaine with subsequent monitoring in the recovery room. In the recovery room, each patient also received 6 mL of 10% hypertonic sodium chloride solution, and 6 mg of non-particulate betamethasone, followed by an injection of 1 mL of sodium chloride solution and removal of the catheter. Multiple outcome measures were utilized including the Numeric Rating Scale (NRS), the Oswestry Disability Index 2.0 (ODI), employment status, and opioid intake with assessment at 3, 6, and 12, 18 and 24 months post treatment. The primary outcome measure was 50% or more improvement in pain scores and ODI scores. Overall, a primary outcome or significant pain relief and functional status improvement of 50% or more was seen in 71% of patients at the end of 2 years. The overall number of procedures over a period of 2 years were 5.7 ± 2.73. The lack of a control group and a prospective design. Significant relief and functional status improvement as seen in 71% of the 70 patients with percutaneous adhesiolysis utilizing local anesthetic steroids and hypertonic sodium chloride solution may be an effective management strategy in patients with chronic function limiting low back and lower extremity pain with central spinal stenosis after failure of conservatie management and fluoroscopically directed epidural injections.


Alocanthedon, a new subgenus of Chalicodoma from Southeast Asia (Hymenoptera, Megachilidae).
A new subgenus, Alocanthedon Engel and Gonzalez subgen. n., is described for five species of unusual Southeast Asian bees in the genus Chalicodoma Lepeletier de Saint Fargeau (Megachilinae: Megachilini). The subgenus is most noteworthy for the deep postgenal depression or furrow in males (bordered outwardly near the base of the mandible by a protuberant, thick lamella) and the presence of a dense patch of black setae posteriorly in the forewing medial cell (except in one species) [resembling the dense patch of setae among the submarginal cells of Thrinchostoma Saussure (Halictidae: Halictinae: Halictini)]. The subgenus is characterized and distinguished from the related Callomegachile Michener. A key to the following five species presently included in the subgenus is provided: Chalicodoma aterrimum (Smith), Chalicodoma atratiforme (Meade-Waldo) comb. n., Chalicodoma memecylonae Engel sp. n., Chalicodoma odontophorum Engel sp. n., and Chalicodoma apoicola Engel sp. n.Chalicodoma (Callomegachile) atratiforme sininsulae (Cockerell) is newly placed in synonymy with C. (C.) fulvipenne (Smith). Species have been collected from Memecylaceae (Myrtales) and Fabaceae (Fabales). The phylogenetic relationships of Alocanthedon among other Megachilini are briefly elaborated upon.


CD8+ Foxp3+ T cells share developmental and phenotypic features with classical CD4+ Foxp3+ regulatory T cells but lack potent suppressive activity.
"Suppressor T cells" were historically defined within the CD8(+) T-cell compartment and recent studies have highlighted several naturally occurring CD8(+) Foxp3(-) Treg populations. However, the relevance of CD8(+) Foxp3(+) T cells, which represent a minor population in both thymi and secondary lymphoid organs of nonmanipulated mice, remains unclear. We here demonstrate that de novo Foxp3 induction in peripheral CD8(+) Foxp3(-) T cells is counter-regulated by DC-mediated co-stimulation via CD80/CD86. CD8(+) Foxp3(+) T cells fail to develop in TCR-transgenic mice with Rag1(-/-) background, similar to classical CD4(+) Foxp3(+) Tregs. Notably, both naturally occurring and induced CD8(+) Foxp3(+) T cells express bona fide Treg markers including CD25, GITR, CTLA4 and CD103, and show defective IFN-γ production upon restimulation when compared with their CD8(+) Foxp3(-) counterparts. However, utilizing DEREG transgenic mice for the isolation of Foxp3(+) cells by eGFP reporter expression, we demonstrate that induced CD8(+) Foxp3(+) T cells similar to activated CD8(+) Foxp3(-) T cells only mildly suppress T-cell proliferation and IFN-γ production. We therefore categorize CD8(+) Foxp3(+) T cells as a tightly controlled population sharing certain developmental and phenotypic properties with classical CD4(+) Foxp3(+) Tregs, but lacking potent suppressive activity.


Physiological ecology of the mangrove-dwelling varanid Varanus indicus.
Some species of terrestrial lizards in wet-dry tropical climates reduce their body temperatures (T(b)'s) and activity and lower their metabolic rates during the dry season when food and water resources are scarce. However, semiaquatic lizards have access to water and presumably food throughout the year, so it is possible that they will not have the seasonal response seen in terrestrial species. We studied the thermal biology, energetics, and water flux of Varanus indicus, a semiaquatic, mangrove-dwelling varanid in tropical northern Australia. Although V. indicus remained active all year, they reduced their activity in the dry season, but not to the extent of terrestrial varanids. Varanus indicus field metabolic rates decreased by 38% in the dry season mostly as a result of the reduction in activity. Although food and water depletion are the driving forces behind decreases in dry season T(b) selection and energetics for many varanids, V. indicus appears not to be subject to these pressures to the same extent. Thermoregulatory indices indicate that V. indicus actively thermoregulate in the wet and dry seasons, but they do not fully exploit the available thermal resources. These lizards are unusual among varanid lizards in that their midday T(b)'s are relatively low (about 31 degrees C) despite the availability of thermal resources that would allow them to attain substantially higher T(b)'s.


[Predictive value of serological tests in the diagnosis of celiac disease].
In the diagnostic work-up of celiac disease (CD) the simpler enzyme-linked immunosorbent assay (ELISA) for the identification of serum anti-transglutaminase (tTG) autoantibodies could substitute the immunofluorescence technique used for the detection of anti-endomysial antibodies (EmA). However, most of the studies on anti-tTG assay have considered pre-selected groups of patients and not consecutive subjects with suspected CD. The aim of this study was to compare the sensitivity, specificity and predictive value of anti-gliadin antibodies (AGA), EmA and two anti-tTG ELISAs, one based on guinea pig (gp)-tTG and the other on human (h)-tTG as antigens, in consecutive patients investigated for suspected CD. The study included 130 consecutive patients (age range 16-84 years), who underwent intestinal biopsy for suspected CD. They presented with one or more of the following symptoms: weight loss, anemia, chronic diarrhea, abdominal pain, dyspepsia, alternating bowel habits and constipation. At the time of admission in the study, an intestinal biopsy was performed and a serum sample was taken for immunoglobulin (Ig) G and IgA AGA, IgA EmA, anti-gp-tTG and anti-h-TG determination. Intestinal histology revealed that 15 patients had partial or total villous atrophy. In these patients the diagnosis of CD was confirmed at subsequent follow-up. The remaining 115 patients included in the study had an intestinal histology characterized by a normal villi/crypts ratio and were considered as controls. Serum EmA, anti-gp-tTG, and anti-h-tTG were positive in all the 15 CD subjects, whereas IgG and IgA AGA were positive in 10/15; in the control group, none were positive for serum EmA, but 11/115 (10%) were positive for anti-gp-tTG and 6/115 (5%) were positive for anti-h-tTG. The sensitivity was 100% for EmA, gp-tTG and h-tTG and 66% for IgA and IgG AGA. The specificity was 100% for EmA, 90% for anti-gp-tTG, 95% for anti-h-tTG, 74% for IgG AGA and 87% for IgA AGA. The negative predictive value was 100% for EmA, anti-h-tTG and anti-gp-tTG, 94% for IgG AGA and 95% for IgA AGA. The positive predictive value was 100% for EmA, 71% for anti-h-tTG (p = 0.03 vs EmA) and 58% for anti-gp-tTG (p = 0.003 vs EmA). Most of the patients who were false positive for anti-tTG had Crohn's disease or chronic liver disease. In conclusion, although both the anti-tTG ELISAs evaluated in the present study showed an optimum sensitivity, their low specificity determined positive predictive values which were significantly lower than those of EmA assay. Besides, the positive predictive value of gp-tTG was too low to warrant submitting a patient to intestinal biopsy for suspected CD.


The foraging ecology of the mountain long-eared bat Plecotus macrobullaris revealed with DNA mini-barcodes.
Molecular analysis of diet overcomes the considerable limitations of traditional techniques for identifying prey remains in bat faeces. We collected faeces from individual Mountain Long-eared Bats Plecotus macrobullaris trapped using mist nets during the summers of 2009 and 2010 in the Pyrenees. We analysed their diet using DNA mini-barcodes to identify prey species. In addition, we inferred some basic features of the bat's foraging ecology that had not yet been addressed. P. macrobullaris fed almost exclusively on moths (97.8%). As prey we detected one dipteran genus (Tipulidae) and 29 moth taxa: 28 were identified at species level (23 Noctuidae, 1 Crambidae, 1 Geometridae, 1 Pyralidae, 1 Sphingidae, 1 Tortricidae), and one at genus level (Rhyacia sp., Noctuidae). Known ecological information about the prey species allowed us to determine that bats had foraged at elevations between 1,500 and 2,500 m amsl (above mean sea level), mostly in subalpine meadows, followed by other open habitats such as orophilous grasslands and alpine meadows. No forest prey species were identified in the diet. As 96.4% of identified prey species were tympanate moths and no evidence of gleaning behaviour was revealed, we suggest P. macrobullaris probably forages by aerial hawking using faint echolocation pulses to avoid detection by hearing moths. As we could identify 87.8% of the analysed sequences (64.1% of the MOTUs, Molecular Operational Taxonomic Units) at species level, we conclude that DNA mini-barcodes are a very useful tool to analyse the diet of moth-specialist bats.


Nuts and their Effect on Gut Microbiota, Gut Function and Symptoms in Adults: A Systematic Review and Meta-Analysis of Randomised Controlled Trials.
Nuts contain fibre, unsaturated fatty acids and polyphenols that may impact the composition of the gut microbiota and overall gut health. This study aimed to assess the impact of nuts on gut microbiota, gut function and gut symptoms via a systematic review and meta-analysis of randomised controlled trials (RCTs) in healthy adults. Eligible RCTs were identified by systematic searches of five electronic databases, hand searching of conference abstracts, clinical trials databases, back-searching reference lists and contact with key stakeholders. Eligible studies were RCTs administering tree nuts or peanuts in comparison to control, measuring any outcome related to faecal microbiota, function or symptoms. Two reviewers independently screened papers, performed data extraction and risk of bias assessment. Outcome data were synthesised as weighted mean difference (WMD) or standardised mean difference (SMD) using a random effects model. This review was registered on PROSPERO (CRD42019138169). Eight studies reporting nine RCTs were included, investigating almonds (n = 5), walnuts (n = 3) and pistachios (n = 1). Nut consumption significantly increased Clostridium (SMD: 0.40; 95% CI, 0.10, 0.71; p = 0.01), Dialister (SMD: 0.44; 95% CI, 0.13, 0.75; p = 0.005), Lachnospira (SMD: 0.33; 95% CI, 0.02, 0.64; p = 0.03) and Roseburia (SMD: 0.36; 95% CI, 0.10, 0.62; p = 0.006), and significantly decreased Parabacteroides (SMD: -0.31; 95% CI, -0.62, -0.00; p = 0.05). There was no effect of nuts on bacterial phyla, diversity or stool output. Further parallel design RCTs, powered to detect changes in faecal microbiota and incorporating functional and clinical outcomes, are needed.


Role of heat accumulation on the incubation effect in multi-shot laser ablation of stainless steel at high repetition rates.
We study the incubation effect during laser ablation of stainless steel with ultrashort pulses to boost the material removal efficiency at high repetition rates. The multi-shot ablation threshold fluence has been estimated for two pulse durations, 650-fs and 10-ps, in a range of repetition rates from 50 kHz to 1 MHz. Our results show that the threshold fluence decreases with the number of laser pulses N due to damage accumulation mechanisms, as expected. Moreover, approaching the MHz regime, the onset of heat accumulation enhances the incubation effect, which is in turn lower for shorter pulses at repetition rates below 600 kHz. A saturation of the threshold fluence value is shown to occur for a significantly high number of pulses, and well fitted by a modified incubation model.


The NBPF1 promoter has been recruited from the unrelated EVI5 gene before simian radiation.
Most new genes arise through the duplication of existing genes. In most cases, the duplication is not limited to the coding sequence but encompasses the regulatory region as well. The NBPF gene family has expanded during recent primate evolution, and it has no known mouse ortholog. One of its members, NBPF1, was found to be disrupted by a constitutional translocation in a neuroblastoma patient. Here, we show that the ancestral NBPF gene copied the regulatory region from an unrelated gene, EVI5, after the split between simians and prosimians but before simian radiation. Phylogenetic analysis points to the possible involvement of positive selection acting on the NBPF1 promoter in the simian lineage. We previously showed decreased NBPF1 expression in certain neuroblastoma cell lines. Here, we show that this expression pattern is mimicked by the EVI5 gene, but partly by different mechanisms. Epigenetic regulation of the EVI5 promoter is common in neuroblastoma cell lines, but it is not for the NBPF promoters. Here, we describe the recent acquisition of the NBPF1 promoter from an unrelated gene, and remarkably, both the donor (EVI5) and acceptor (NBPF1) genes are disrupted by constitutional translocations in patients with neuroblastoma, suggesting a functional link between these genes and the disease.


The deep sea is a major sink for microplastic debris.
Marine debris, mostly consisting of plastic, is a global problem, negatively impacting wildlife, tourism and shipping. However, despite the durability of plastic, and the exponential increase in its production, monitoring data show limited evidence of concomitant increasing concentrations in marine habitats. There appears to be a considerable proportion of the manufactured plastic that is unaccounted for in surveys tracking the fate of environmental plastics. Even the discovery of widespread accumulation of microscopic fragments (microplastics) in oceanic gyres and shallow water sediments is unable to explain the missing fraction. Here, we show that deep-sea sediments are a likely sink for microplastics. Microplastic, in the form of fibres, was up to four orders of magnitude more abundant (per unit volume) in deep-sea sediments from the Atlantic Ocean, Mediterranean Sea and Indian Ocean than in contaminated sea-surface waters. Our results show evidence for a large and hitherto unknown repository of microplastics. The dominance of microfibres points to a previously underreported and unsampled plastic fraction. Given the vastness of the deep sea and the prevalence of microplastics at all sites we investigated, the deep-sea floor appears to provide an answer to the question-where is all the plastic?


What makes a rhythm complex? The influence of musical training and accent type on beat perception.
Perception of a regular beat in music is inferred from different types of accents. For example, increases in loudness cause intensity accents, and the grouping of time intervals in a rhythm creates temporal accents. Accents are expected to occur on the beat: when accents are "missing" on the beat, the beat is more difficult to find. However, it is unclear whether accents occurring off the beat alter beat perception similarly to missing accents on the beat. Moreover, no one has examined whether intensity accents influence beat perception more or less strongly than temporal accents, nor how musical expertise affects sensitivity to each type of accent. In two experiments, we obtained ratings of difficulty in finding the beat in rhythms with either temporal or intensity accents, and which varied in the number of accents on the beat as well as the number of accents off the beat. In both experiments, the occurrence of accents on the beat facilitated beat detection more in musical experts than in musical novices. In addition, the number of accents on the beat affected beat finding more in rhythms with temporal accents than in rhythms with intensity accents. The effect of accents off the beat was much weaker than the effect of accents on the beat and appeared to depend on musical expertise, as well as on the number of accents on the beat: when many accents on the beat are missing, beat perception is quite difficult, and adding accents off the beat may not reduce beat perception further. Overall, the different types of accents were processed qualitatively differently, depending on musical expertise. Therefore, these findings indicate the importance of designing ecologically valid stimuli when testing beat perception in musical novices, who may need different types of accent information than musical experts to be able to find a beat. Furthermore, our findings stress the importance of carefully designing rhythms for social and clinical applications of beat perception, as not all listeners treat all rhythms alike.


Breaking the Vicious Cycle of Antibiotic Killing and Regrowth of Biofilm-Residing Pseudomonas aeruginosa.
Biofilm-residing bacteria embedded in an extracellular matrix are protected from diverse physicochemical insults. In addition to the general recalcitrance of biofilm bacteria, high bacterial loads in biofilm-associated infections significantly diminish the efficacy of antimicrobials due to a low per-cell antibiotic concentration. Accordingly, present antimicrobial treatment protocols that have been established to serve the eradication of acute infections fail to clear biofilm-associated chronic infections. In the present study, we applied automated confocal microscopy on Pseudomonas aeruginosa to monitor dynamic killing of biofilm-grown bacteria by tobramycin and colistin in real time. We revealed that the time required for surviving bacteria to repopulate the biofilm could be taken as a measure for effectiveness of the antimicrobial treatment. It depends on the (i) nature and concentration of the antibiotic, (ii) duration of antibiotic treatment, (iii) application as monotherapy or combination therapy, and (iv) interval of drug administration. The vicious cycle of killing and repopulation of biofilm bacteria could also be broken in an in vivo model system by applying successive antibiotic dosages at intervals that do not allow full reconstitution of the biofilm communities. Treatment regimens that consider the important aspects of antimicrobial killing kinetics bear the potential to improve control of biofilm regrowth. This is an important and underestimated factor that is bound to ensure sustainable treatment success of chronic infections.


Inhibition of DYRK1A Stimulates Human β-Cell Proliferation.
Restoring functional β-cell mass is an important therapeutic goal for both type 1 and type 2 diabetes (1). While proliferation of existing β-cells is the primary means of β-cell replacement in rodents (2), it is unclear whether a similar principle applies to humans, as human β-cells are remarkably resistant to stimulation of division (3,4). Here, we show that 5-iodotubercidin (5-IT), an annotated adenosine kinase inhibitor previously reported to increase proliferation in rodent and porcine islets (5), strongly and selectively increases human β-cell proliferation in vitro and in vivo. Remarkably, 5-IT also increased glucose-dependent insulin secretion after prolonged treatment. Kinome profiling revealed 5-IT to be a potent and selective inhibitor of the dual-specificity tyrosine phosphorylation-regulated kinase (DYRK) and cell division cycle-like kinase families. Induction of β-cell proliferation by either 5-IT or harmine, another natural product DYRK1A inhibitor, was suppressed by coincubation with the calcineurin inhibitor FK506, suggesting involvement of DYRK1A and nuclear factor of activated T cells signaling. Gene expression profiling in whole islets treated with 5-IT revealed induction of proliferation- and cell cycle-related genes, suggesting that true proliferation is induced by 5-IT. Furthermore, 5-IT promotes β-cell proliferation in human islets grafted under the kidney capsule of NOD-scid IL2Rg(null) mice. These results point to inhibition of DYRK1A as a therapeutic strategy to increase human β-cell proliferation.


A Single Primary Blast-Induced Traumatic Brain Injury in a Rodent Model Causes Cell-Type Dependent Increase in Nicotinamide Adenine Dinucleotide Phosphate Oxidase Isoforms in Vulnerable Brain Regions.
Blast-induced traumatic brain injury (bTBI) is a leading cause of morbidity in soldiers on the battlefield and in training sites with long-term neurological and psychological pathologies. Previous studies from our laboratory demonstrated activation of oxidative stress pathways after blast injury, but their distribution among different brain regions and their impact on the pathogenesis of bTBI have not been explored. The present study examined the protein expression of two isoforms: nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 1 and 2 (NOX1, NOX2), corresponding superoxide production, a downstream event of NOX activation, and the extent of lipid peroxidation adducts of 4-hydroxynonenal (4HNE) to a range of proteins. Brain injury was evaluated 4 h after the shock-wave exposure, and immunofluorescence signal quantification was performed in different brain regions. Expression of NOX isoforms displayed a differential increase in various brain regions: in hippocampus and thalamus, there was the highest increase of NOX1, whereas in the frontal cortex, there was the highest increase of NOX2 expression. Cell-specific analysis of changes in NOX expression with respect to corresponding controls revealed that blast resulted in a higher increase of NOX1 and NOX 2 levels in neurons compared with astrocytes and microglia. Blast exposure also resulted in increased superoxide levels in different brain regions, and such changes were reflected in 4HNE protein adduct formation. Collectively, this study demonstrates that primary blast TBI induces upregulation of NADPH oxidase isoforms in different regions of the brain parenchyma and that neurons appear to be at higher risk for oxidative damage compared with other neural cells.


Exciton photoluminescence in resonant quasi-periodic Thue-Morse quantum wells.
This Letter investigates exciton photoluminescence (PL) in resonant quasi-periodic Thue-Morse quantum wells (QWs). The results show that the PL properties of quasi-periodic Thue-Morse QWs are quite different from those of resonant Fibonacci QWs. The maximum and minimum PL intensities occur under the anti-Bragg and Bragg conditions, respectively. The maxima of the PL intensity gradually decline when the filling factor increases from 0.25 to 0.5. Accordingly, the squared electric field at the QWs decreases as the Thue-Morse QW deviates from the anti-Bragg condition.


Natural decomposition of hornbeam wood decayed by the white rot fungus Trametes versicolor.
The impacts of white-rot fungi on altering wood chemistry have been studied mostly in vitro. However, in vivo approaches may enable better assessment of the nature of interactions between saprotrophic fungi and host tree in nature. Hence, decayed and sound wood samples were collected from a naturally infected tree (Carpinus betulus L.). Fruiting bodies of the white rot fungus Trametes versicolor grown on the same tree were identified using rDNA ITS sequencing. Chemical compositions (cellulose and lignin) of both sound and infected wood were studied. FT-IR spectroscopy was used to collect spectra of decayed and un-decayed wood samples. The results of chemical compositions indicated that T. versicolor reduced cellulose and lignin in similar quantities. Fungal activities in decayed wood causes serious decline in pH content. The amount of alcohol-benzene soluble extractives was severely decreased, while a remarkable increase was found in 1% sodium hydroxide soluble and hot water extractive contents in the decayed wood samples, respectively. FT-IR analyses demonstrated that T. versicolor causes simultaneous white rot in the hornbeam tree in vivo which is in line with in vitro experiments.


Thoracic and lumbar pedicle morphometry in achondroplasia.
For safe pedicle screw insertion, knowing pedicle anatomy is essential. Pedicle morphometry in achondroplasia has not been quantitatively described. Therefore, we analyzed 302 thoracic and lumbar pedicles in 11 patients using computed tomography. Transverse endosteal diameter, screw path length, transverse angle, sagittal diameter, and sagittal angle were calculated. We analyzed for safe screw length, size, and trajectory. The data were compared with that on healthy people of different races. In patients with achondroplasia, the maximum endosteal diameter was at L5 and the minimum was at T5. Screw path length was longest at L2 and shortest at T2. Most dimensions were smaller compared with those of healthy people. Abnormal anteromedial transverse angulations were observed between T11 to L2. The maximum transverse angulations were at T2. Sagittal diameter was largest at T12 and smallest at T5. The maximum sagittal angle was seen at T2, and at L5 it was caudal. At all levels except L5, the transverse diameter is the limiting factor for screw size. Six-millimeter screws can be used at L5. Screws that are 35 mm or less are safe to use between T7 to L5. There are surgically important differences in the different angles and diameters of thoracic and lumbar pedicles of patients with achondroplasia and those of healthy people.


A review of flexible lithium-sulfur and analogous alkali metal-chalcogen rechargeable batteries.
Flexible energy storage systems are imperative for emerging flexible devices that are revolutionizing our life. Lithium-ion batteries, the current main power sources, are gradually approaching their theoretical limitation in terms of energy density. Therefore, alternative battery chemistries are urgently required for next-generation flexible power sources with high energy densities, low cost, and inherent safety. Flexible lithium-sulfur (Li-S) batteries and analogous flexible alkali metal-chalcogen batteries are of paramount interest owing to their high energy densities endowed by multielectron chemistry. In this review, we summarized the recent progress of flexible Li-S and analogous batteries. A brief introduction to flexible energy storage systems and general Li-S batteries has been provided first. Progress in flexible materials for flexible Li-S batteries are reviewed subsequently, with a detailed classification of flexible sulfur cathodes as those based on carbonaceous (e.g., carbon nanotubes, graphene, and carbonized polymers) and composite (polymers and inorganics) materials and an overview of flexible lithium anodes and flexible solid-state electrolytes. Advancements in other flexible alkali metal-chalcogen batteries are then introduced. In the next part, we emphasize the importance of cell packaging and flexibility evaluation, and two special flexible battery prototypes of foldable and cable-type Li-S batteries are highlighted. In the end, existing challenges and future development of flexible Li-S and analogous alkali metal-chalcogen batteries are summarized and prospected.


Development of refractive errors into old age.
To evaluate refractive errors in older adults. The distribution of refractive error components was evaluated in a sample of 569 older adults including 171 participants over the age of 80 years. The mean age was 75.2 years with a range from 59 to 106 years. Emphasis was placed on modern methods of analyzing astigmatic refractive errors, which convert cylindrical refractive errors into primary and oblique components. The known increase in hyperopia after maturity continues into old age. The primary negative astigmatic component increases dramatically in prevalence and amount after age 70 years, whereas the oblique component remains unchanged. Significant anisometropia is common in the oldest old, suggesting failure of emmetropization mechanisms with age. Substantial gender differences exist in refractive changes with age. The continuing changes in all components of refractive error into old age and the surprisingly high prevalence of large amounts of astigmatism and anisometropia emphasize the importance of regular refractive evaluations among the oldest old.


A perspective on the mechanism of the light-rise of the electrooculogram.
The light-rise of the electrooculogram is believed to originate from a substance released from the rods after dark adaptation. The identity of this "elusive" light-rise substance has not been demonstrated, and therefore a new perspective on the light-rise is presented. The light-rise is caused by the depolarization of the basolateral membrane of the retinal pigment epithelium (RPE) has become clearer in the last decade with the identification of calcium as the intracellular secondary messenger and the role of bestrophin as a regulator of intracellular stores of calcium and controlling the cytosolic calcium levels through L-type calcium channels. The light-rise depends upon a change from darkness to light, which triggers the intracellular cascade resulting in the depolarization of the basolateral membrane. The same intracellular signaling molecules, notably calcium and inositol triphosphate (IP3), are strongly implicated in this cascade. Recent studies have now led to a clearer understanding of the roles and functions of the ion channels and their contribution to the light-rise with IP3 regulating the release of calcium for intracellular stores. Given that calcium and IP3 are also regulators of phagocytosis, and that the initiation of rod outer segment phagocytosis is initiated with light-onset, it may be that the light-rise is generated in response to this physiological event. Therefore, the putative light-rise substance may not be released by the rods, but follow directly from IP3 release from the RPE's phospholipid membrane following the onset of light and the initiation of phagocytosis. The light rise substance, could be considered to be light itself.


Search for heavy particles decaying into top-quark pairs using lepton-plus-jets events in proton-proton collisions at s = 13 TeV with the ATLAS detector.
A search for new heavy particles that decay into top-quark pairs is performed using data collected from proton-proton collisions at a centre-of-mass energy of 13 TeV by the ATLAS detector at the Large Hadron Collider. The integrated luminosity of the data sample is 36.1 fb - 1 . Events consistent with top-quark pair production are selected by requiring a single isolated charged lepton, missing transverse momentum and jet activity compatible with a hadronic top-quark decay. Jets identified as likely to contain b-hadrons are required to reduce the background from other Standard Model processes. The invariant mass spectrum of the candidate top-quark pairs is examined for local excesses above the background expectation. No significant deviations from the Standard Model predictions are found. Exclusion limits are set on the production cross-section times branching ratio for hypothetical Z ' bosons, Kaluza-Kein gluons and Kaluza-Klein gravitons that decay into top-quark pairs.


Detection of malingering on the Halstead-Reitan Battery: a cross-validation.
Using the Halstead-Reitan Battery profiles of 796 people, a formula for the detection of malingering was cross-validated to assess the false positive rate. Subjects included normals, psychiatric cases, and all major types of organics. The formula incorrectly designated 27% of the sample as fakers (i.e., as false positives). Of the 120 head trauma cases, 27 (22.5%) obtained Fake scores, while 93 (77.5%) were correctly assessed as not malingering.


Modulation of the trafficking efficiency and functional properties of ATP-sensitive potassium channels through a single amino acid in the sulfonylurea receptor.
Mutations in the sulfonylurea receptor 1 (SUR1), a subunit of ATP-sensitive potassium (K(ATP)) channels, cause familial hyperinsulinism. One such mutation, deletion of phenylalanine 1388 (DeltaPhe-1388), leads to defects in both trafficking and MgADP response of K(ATP) channels. Here we investigated the biochemical features of Phe-1388 that control the proper trafficking and function of K(ATP) channels by substituting the residue with all other 19 amino acids. Whereas surface expression is largely dependent on hydrophobicity, channel response to MgADP is governed by multiple factors and involves the detailed architecture of the amino acid side chain. Thus, structural features in SUR1 required for proper channel function are distinct from those required for correct protein trafficking. Remarkably, replacing Phe-1388 by leucine profoundly alters the physiological and pharmacological properties of the channel. The F1388L-SUR1 channel has increased sensitivity to MgADP and metabolic inhibition, decreased sensitivity to glibenclamide, and responds to both diazoxide and pinacidil. Because this conservative amino acid substitution occurs in the SUR2A and SUR2B isoforms, the mutation provides a mechanism by which functional diversities in K(ATP) channels are generated.


SeqWare Query Engine: storing and searching sequence data in the cloud.
Since the introduction of next-generation DNA sequencers the rapid increase in sequencer throughput, and associated drop in costs, has resulted in more than a dozen human genomes being resequenced over the last few years. These efforts are merely a prelude for a future in which genome resequencing will be commonplace for both biomedical research and clinical applications. The dramatic increase in sequencer output strains all facets of computational infrastructure, especially databases and query interfaces. The advent of cloud computing, and a variety of powerful tools designed to process petascale datasets, provide a compelling solution to these ever increasing demands. In this work, we present the SeqWare Query Engine which has been created using modern cloud computing technologies and designed to support databasing information from thousands of genomes. Our backend implementation was built using the highly scalable, NoSQL HBase database from the Hadoop project. We also created a web-based frontend that provides both a programmatic and interactive query interface and integrates with widely used genome browsers and tools. Using the query engine, users can load and query variants (SNVs, indels, translocations, etc) with a rich level of annotations including coverage and functional consequences. As a proof of concept we loaded several whole genome datasets including the U87MG cell line. We also used a glioblastoma multiforme tumor/normal pair to both profile performance and provide an example of using the Hadoop MapReduce framework within the query engine. This software is open source and freely available from the SeqWare project (http://seqware.sourceforge.net). The SeqWare Query Engine provided an easy way to make the U87MG genome accessible to programmers and non-programmers alike. This enabled a faster and more open exploration of results, quicker tuning of parameters for heuristic variant calling filters, and a common data interface to simplify development of analytical tools. The range of data types supported, the ease of querying and integrating with existing tools, and the robust scalability of the underlying cloud-based technologies make SeqWare Query Engine a nature fit for storing and searching ever-growing genome sequence datasets.


Automated quality control and cell identification of droplet-based single-cell data using dropkick.
A major challenge for droplet-based single-cell sequencing technologies is distinguishing true cells from uninformative barcodes in data sets with disparate library sizes confounded by high technical noise (i.e., batch-specific ambient RNA). We present dropkick, a fully automated software tool for quality control and filtering of single-cell RNA sequencing (scRNA-seq) data with a focus on excluding ambient barcodes and recovering real cells bordering the quality threshold. By automatically determining data set-specific training labels based on predictive global heuristics, dropkick learns a gene-based representation of real cells and ambient noise, calculating a cell probability score for each barcode. Using simulated and real-world scRNA-seq data, we benchmarked dropkick against conventional thresholding approaches and EmptyDrops, a popular computational method, showing greater recovery of rare cell types and exclusion of empty droplets and noisy, uninformative barcodes. We show for both low- and high-background data sets that dropkick's weakly supervised model reliably learns which genes are enriched in ambient barcodes and draws a multidimensional boundary that is more robust to data set-specific variation than existing filtering approaches. dropkick provides a fast, automated tool for reproducible cell identification from scRNA-seq data that is critical to downstream analysis and compatible with popular single-cell Python packages.


Methodological approaches for a systematic review of end-of-life care.
As background for a National Institutes of Health State of the Science Conference on End-of-Life-Care, we performed a systematic review of end-of-life care and outcomes. The systematic review was intended to evaluate the evidence in the field from the perspective of concerns important to patients, caregivers, and the health care system. This article relates the challenges in performing a systematic review of end-of-life care and outcomes, and describes the methods that we used to define the scope, search the literature, develop exclusion and inclusion criteria, incorporate various types of articles, and synthesize the results. Major challenges to conducting a review included the need to define "end of life," clarify a conceptual framework of outcomes including definitions of terms and the relationships among terms, and determine specific goals for the review. The review identified 24,423 total citations, of which 911 comprised the final set used for the evidence report. This very large, diverse body of literature reflects the tremendous growth of the field of end-of-life care over the last decade.


Multicenter phase II study to evaluate a 28-day regimen of oral fluorouracil plus eniluracil in the treatment of patients with previously untreated metastatic colorectal cancer.
To determine the efficacy of fluorouracil (5-FU) plus eniluracil when administered to patients with previously untreated metastatic colorectal cancer. In this single-arm phase II study, patients with previously untreated metastatic colorectal cancer received oral eniluracil plus 5-FU (10:1 dose ratio), at 5-FU doses of 1.00 mg/m(2) or 1.15 mg/m(2) twice daily (every 12 hours) for 28 consecutive days repeated every 5 weeks (one cycle). Treatment continued until there was documented disease progression or unacceptable toxicity. Thirty and 25 patients were enrolled at a starting dose of 1.00 mg/m(2) and 1.15 mg/m(2), respectively. Fourteen (25%) of 55 patients (95% confidence interval, 15% to 39%) had a partial response, and 20 patients (36%) had stable disease. The median durations of the partial responses and stable disease were 23.9 weeks (range, 12.3 to 52.1+ weeks) and 24.1 weeks (range, 17.1 to 55.6+ weeks), respectively. The median durations of progression-free and overall survival were 22.6 weeks (range, 21.0 to 29.0 weeks) and 59 weeks (range, 4 to 84+ weeks), respectively. The response rate in the 1.15 mg/m(2)-dose group was similar to the 1.00 mg/m(2)-dose group (28% v 23%, respectively). Severe (grade 3/4) nonhematologic treatment-related toxicity included diarrhea (nine patients), nausea/vomiting (one patient each), mucositis (two patients), and anorexia (one patient). Severe hematologic toxicities were rare. At the 1.15 mg/m(2)-dose level, two patients exhibited grade 3 granulocytopenia, and two patients had grade 3 anemia. The response rate with oral 5-FU plus eniluracil is comparable with that observed with infusional 5-FU or bolus 5-FU and leucovorin. The toxicity profile of this oral regimen is acceptable for use in an outpatient home-based setting.


Cognitive research in zoo-housed chimpanzees: influence of personality and impact on welfare.
We monitored chimpanzee welfare during the introduction of on-exhibit cognitive research training and testing, as measured by behavior and interest in such training, and related individual variation to personality assessments. We observed 11 chimpanzees (six males; five females) over a 16-month period and compared their behavior across three conditions: (1) Baseline (nontraining/research situations) and (2) an on-going, off-exhibit program of Husbandry Training and (3) Research Pod Activities, on-exhibit, group training for cognitive testing. There was considerable individual variation in their interest levels during research sessions; females and those scoring higher for Openness were present more frequently (including those who actively participated and those who observed others participating), but interest did not vary in relation to rates of self-directed behaviors (SDBs), rank, or the level of social disruptions within the group (i.e. large-scale displays or fights). The frequency of SDBs was predicted by the Neuroticism personality factor, but did not differ across baseline and training contexts, indicating that these activities do not negatively impact welfare. We also explored vigilance as an indicator of social uncertainty, but social monitoring did not differ in relation to either social context or rank. Finally, we explored how the specific characteristics of the research context impacted on SDBs; namely, social context, reward contingency, and visual access to keepers. SDBs increased only when visual access to keepers was restricted, suggesting that visual contact reduced uncertainty in novel training contexts. Overall, the introduction of a cognitive research program did not compromise welfare, and the chimpanzees' repeated interest and willingness to participate suggests that the research was enriching.


Static Rashba Effect by Surface Reconstruction and Photon Recycling in the Dynamic Indirect Gap of APbBr3 (A = Cs, CH3NH3) Single Crystals.
Recently, halide perovskites have gained significant attention from the perspective of efficient spintronics owing to the Rashba effect. This effect occurs as a consequence of strong spin-orbit coupling under a noncentrosymmetric environment, which can be dynamic and/or static. However, there exist intense debates on the origin of broken inversion symmetry since the halide perovskites typically crystallize into a centrosymmetric structure. In order to clarify the issue, we examine both dynamic and static effects in the all-inorganic CsPbBr3 and organic-inorganic CH3NH3PbBr3 (MAPbBr3) perovskite single crystals by employing temperature- and polarization-dependent photoluminescence excitation spectroscopy. The perovskite single crystals manifest the dynamic effect by photon recycling in the indirect Rashba gap, causing dual peaks in the photoluminescence. However, the effect vanishes in CsPbBr3 at low temperatures (<50 K) accompanied by a striking color change of the crystal, arising presumably from lower degrees of freedom for inversion symmetry breaking associated with the thermal motion of the spherical Cs cation compared with the polar MA cation in MAPbBr3. We also show that the static Rashba effect occurs only in MAPbBr3 below 90 K, presumably due to surface reconstruction via MA-cation ordering, which likely extends across a few layers from the crystal surface to the interior. We further demonstrate that this static Rashba effect can be completely suppressed upon surface treatment with polymethyl methacrylate (PMMA) coating. We believe that our results provide a rationale for the Rashba effects in halide perovskites.