Miracle-dz/UniFAR-FTUs huggingface dataset:
Anaerobic methane oxidizing archaea offset sediment methane concentrations in Arctic thermokarst lagoons

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4 concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, and lipid biomarkers. We specifically assessed whether sulfate-driven anaerobic methane oxidation (S-AOM) through anaerobic methanotrophic archaea (ANMEs), common in marine sediments with constant supply of sulfate and methane, establish after thermokarst lagoon development and whether sulfate-driven ANMEs consequently oxidize CH4 that would be emitted to the water column under thermokarst lake conditions. The marine-influenced lagoon environment had fundamentally different methane-cycling microbial communities and metabolic pathways compared to the freshwater lakes, suggesting a substantial reshaping of microbial and carbon dynamics during lagoon formation. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow. CH4 concentrations in the freshwater-influenced sediments averaged 1.34±0.98 µmol g−1, with highly depleted δ13C-CH4 values ranging from -89‰ to -70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH4 concentrations of 0.011±0.005 µmol g−1 with comparatively enriched δ13C-CH4 values of -54‰ to -37‰ pointing to substantial methane oxidation. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of porewater chemistry and depth. This potentially contributed to the high CH4 concentrations observed in all sulfate-poor sediments. Our study shows that S-AOM in lagoon sediments can effectively reduce sediment CH4 concentrations and we conclude that thermokarst lake to lagoon transitions have the potential to mitigate terrestrial methane fluxes before thermokarst lakes fully transition to a marine environment.
Transcriptome analysis of FOXO-dependent hypoxia gene expression identifies Hipk as a regulator of low oxygen tolerance in Drosophila

When exposed to low oxygen or hypoxia, animals must alter their metabolism and physiology to ensure proper cell-, tissue- and whole-body level adaptations to their hypoxic environment. These alterations often involve changes in gene expression. While extensive work has emphasized the importance of the HIF-1 alpha transcription factor on controlling hypoxia gene expression, less is known about other transcriptional mechanisms. We previously identified the transcription factor FOXO as a regulator of hypoxia tolerance in Drosophila larvae and adults. Here we use an RNA-sequencing approach to identify FOXO-dependent changes in gene expression that are associated with these tolerance effects. We found that hypoxia altered the expression of over 2000 genes and that approximately 40% of these gene expression changes required FOXO. We discovered that hypoxia exposure led to a FOXO-dependent increase in genes involved in cell signaling, such as kinases, GTPase regulators, and regulators of the Hippo/Yorkie pathway. Among these, we identified homeodomain-interacting protein kinase (Hipk) as being required for hypoxia survival. We also found that hypoxia suppresses the expression of genes involved in ribosome synthesis and egg production, and we showed that hypoxia suppresses tRNA synthesis and mRNA translation and reduces female fecundity. Among the downregulated genes, we discovered that FOXO was required for suppression of many ribosomal protein genes and genes involved in oxidative phosphorylation, pointing to a role for FOXO in limiting energetically costly processes such as protein synthesis and mitochondrial activity upon hypoxic stress. This work uncovers a widespread role for FOXO in mediating hypoxia changes in gene expression.
Glycan Recognition Diversemolecular recognition properties of blood group A binding monoclonal antibodies

Information about specificity and affinity is critical for use of carbohydrate-binding antibodies. Herein, we evaluated eight monoclonal antibodies to the blood group A (BG-A) antigen. Antibodies 87-G, 9A, HE-10, HE-24, HE-193, HE-195, T36 and Z2A were profiled on a glycan microarray to assess specificity, relative affinity and the influence of glycan density on recognition. Our studies highlight several noteworthy recognition properties. First, most antibodies bound GalNAcα1–3Gal and the BG-A trisaccharide nearly as well as larger BG-A oligosaccharides. Second, several antibodies only bound the BG-A trisaccharide when displayed on certain glycan chains. These first two points indicate that the carrier glycan chains primarily influence selectivity, rather than binding strength. Third, binding of some antibodies was highly dependent on glycan density, illustrating the importance of glycan presentation for recognition. Fourth, some antibodies recognized the tumorassociated Tn antigen, and one antibody only bound the variant composed of a GalNAc-alpha-linked to a serine residue. Collectively, these results provide new insights into the recognition properties of anti-BG-A antibodies.
Practice of Epidemiology Comparison of Parametric and Nonparametric Estimators for the Association Between Incident PrepregnancyObesity and Stillbirth in a Population-Based Cohort Study

While prepregnancy obesity increases risk of stillbirth, few studies have evaluated the role of newly developed obesity independent of long-standing obesity. Additionally, researchers have relied almost exclusively on parametric models, which require correct specification of an unknown function for consistent estimation. We estimated the association between incident obesity and stillbirth in a cohort constructed from linked birth and death records in Pennsylvania (2003–2013). Incident obesity was defined as bodymass index (weight (kg)/height (m)) greater than or equal to 30. We used parametric G-computation, semiparametric inverse-probability weighting, and parametric/ nonparametric targeted minimum loss-based estimation (TMLE) to estimate the association between incident prepregnancy obesity and stillbirth. Compared with pregnancies from women who stayed nonobese, women who became obese prior to their next pregnancy were estimated to have 2.0 (95% confidence interval (CI): 0.5, 3.5) more stillbirths per 1,000 pregnancies using parametric G-computation. However, despite well-behaved stabilized inverse probability weights, risk differences estimated from inverse-probability weighting, nonparametric TMLE, and parametric TMLE represented 6.9 (95% CI: 3.7, 10.0), 0.4 (95% CI: 0.1, 0.7), and 2.9 (95% CI: 1.5, 4.2) excess stillbirths per 1,000 pregnancies, respectively. These results, particularly those derived from nonparametric TMLE, were highly sensitive to covariates included in the propensity score models. Our results suggest that caution is warranted when using nonparametric estimators to quantify exposure effects.
Activation of avb3-Vitronectin Binding Is a Multistage Process in which Increases in Bond Strength Are Dependent on Y747 and Y759 in the Cytoplasmic Domain of b3

Integrin receptors serve as mechanical links between the cell and its structural environment. Using avb3 integrin expressed in K562 cells as a model system, the process by which the mechanical connection between avb3 and vitronectin develops was analyzed by measuring the resistance of these bonds to mechanical separation. Three distinct stages of activation, as defined by increases in the avb3-vitronectin binding strength, were defined by mutational, biochemical, and biomechanical analyses. Activation to the low binding strength stage 1 occurs through interaction with the vitronectin ligand and leads to the phosphorylation of Y747 in the b3 subunit. Stage 2 is characterized by a 4-fold increase in binding strength and is dependent on stage1 and the phosphorylation of Y747. Stage 3 is characterized by a further 2.5-fold increase in binding strength and is dependent on stage 2 events and the availability of Y759 for interaction with cellular proteins. The Y747F mutant blocked the transition from stage 1 to stage 2, and the Y759F blocked the transition from stage 2 to stage 3. The data suggest a model for tension-induced activation of avb3 integrin.
Euler-MacLaurin expansions for lattices above dimension one

On presente un developpement en serie pour evaluer la somme des valeurs prises par une fonction aux points d'un reseau contenu dans un polytope avec sommets dans le reseau ou au moins rationnels par rapport a lui. Le developpement s'exprime au moyen d'integrales d'operateurs differentiels lineaires a coefficients constants appliques a la fonction. Les coefficients sont calcules a partir des volumes des faces et des angles aux sommets. On utilise pour cela de nouvelles algebres, generalisant les anneaux de Chow, mais qui contiennent aussi des donnees infinitesimales sur des varietes. On calcule dans ces algebres les analogues des classes de Todd des varietes toriques.
In Vitro Studies on Callus Induction of Kenaf ( Hibiscus cannabinus L.)

The present study was undertaken to investigate the comparative regeneration potential of seedling explants of kenaf ( Hibiscus cannabinus L.) at the Biotechnology Laboratory, Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, during the period from January, 2014 to June, 2014. An efficient regeneration protocol was developed for kenaf genotypes HC-2, HC-95 and HC-3 using root tip, cotyledon and hypocotyl as explants. For regeneration, Murashige and Skoog (MS) medium was used as culture medium and supplemented with different concentrations and combinations of NAA (α-napthaleneacetic acid) and BAP (6-Benzylaminopurine) as growth regulators. Different concentrations and combinations of hormones for callus induction formation NAA (0.0, 1.0, 1.0, 1.5, 2.0, 2.0 and 2.0 mg/L) and BAP (0.0, 1.0, 2.5, 5.0, 7.5, 10.0 and 15.0 mg/L) were used while, for shoot initiation BAP (0.0, 2.0, 4.0, 6.0, 8.0, 10.0 and 12.0 mg/L) were used. The HC-2 genotype had the highest callus induction (59.14) HC-95 genotype had the lowest value 37.70% for callus induction. The callus induction (71.41%) occurred the best on 2.0 mg/L NAA + 7.5 mg/L BAP combination. On the other hand, hypocotyl explant showed the highest callus induction (60.52%) followed by the other two explants (Root tip and cotyledon) which had lower callus induction (41.27%, 53.49%). The explant from the hypocotyl of genotype HC-2 showed the best performance on callus induction (91.33%) in 2.0 mg/L NAA +7.5 mg/L BAP combination within 7-10 days compared with genotype HC-95 and HC-3. The frequency of variation was found to be genotype dependent. Certain changes were found in regeneration of all the three genotypes, suggesting the existence of a mutation-sensitive part of the kenaf genome and possibility of improvement through somaclonal variation.
I think there is a world market for maybe five quantum computers

In 1943, Thomas J. Watson, chairman of IBM, stated “I think there is a world market for maybe five computers. ” From todays point of view, we can boldly say that this statement could be assessed with a superlative of “wrong” if such a word existed. The main reason for the success story of the (conventional) computer is the fact that it is a general purpose machine. As it can solve problems from a wide range of applications, everyone needs one. At the moment, the situation regarding quantum computers seems to be different. Despite of the fact that the idea of quantum computing was proposed already over 20 years ago by R. Feynman [Fey82], till this day, only a minor amount of applications is covered by quantum algorithms so that we cannot speak of a general purpose machine. Let us have a closer look at some of the most popular problems that should demonstrate the potential strength of the quantum computer.
Invited Editorial: Cutting a Gordian Knot in the Linkage Analysis of Complex Human Traits

ical basis has in recent years seen major successes in that the genes for several diseases have been'localized on the human gene map. However, many of the common and often chronic diseases such as cancer, epilepsy, and psychiatric diseases must pose a much greater challenge, since the majority of these genetically complex traits have so far resisted efforts at identifying and mapping underlying gene loci. There have been only a few
EXPERIMENTAL BACTERIAL ENDOCARDITIS OF IN

SUMMARY. -A method has been developed for assessing metabolic activity of bacteria in the vegetations of bacterial endocarditis using a labelled metabolite and autoradiography. Evidence provided by this technique suggests that there are different degrees of activity between superficial and more deeply placed bacterial colonies, and that variations in activity also exist within a single group of organisms. The possible relevance of these findings to the antibiotic therapy of endocarditis is discussed.
Development and clinical trial of a smartphone-based colorimetric detection system for self-monitoring of blood glucose

Blood glucose measurements help to guide insulin therapy, thus reducing disease severities, secondary complications, and relatedmortalities. Efforts are underway to allowdiabetes patients to experience a more convenient way to measure blood glucose and consequently increase their adherence to regular self-monitoring of blood glucose (SMBG). This study demonstrated a new SMBG system that integrated all components of a glucometer via a smartphone’s optical sensing module to detect the colorimetric blood strip and obtains the blood glucose concentration with calculations performed by an application install in the smartphone. To validate the accuracy and applicability of the new SMBG system regarding the ISO15197:2013 accuracy criteria and patient requirements, a clinical trial and usability survey involving participants from different age groups were conducted in collaboration with the China Medical University, where enrolled 120 diabetic patients were asked to operate the new SMBG system to measure their blood glucose concentration, and feedback was obtained from their user experience. The results showed that three different reagent system lots fulfilled the accuracy requirements with values of 97.4–97.5% , and all of the data were within zones A and B of the consensus error grid, which satisfies the ISO 15197:2013 requirement. The usability survey showed that 97.5% of the participants found the operations convenient, and 100% found the design easy for carrying. This new system could lead to improvements in blood glucose monitoring by people with diabetes, and thus, better management of the disease. © 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement
Practice of Epidemiology How Long-Term Acute Care Hospitals Can Play an Important Role in Controlling Carbapenem-Resistant Enterobacteriaceae in a Region: A Simulation Modeling Study

Typically, long-term acute care hospitals (LTACHs) have less experience in and incentives to implementing aggressive infection control for drug-resistant organisms such as carbapenem-resistant Enterobacteriaceae (CRE) than acute care hospitals. Decision makers need to understand how implementing control measures in LTACHs can impact CRE spread regionwide. Using our Chicago metropolitan region agent-based model to simulate CRE spread and control, we estimated that a prevention bundle in only LTACHs decreased prevalence by a relative 4.6%–17.1%, averted 1,090–2,795 new carriers, 273–722 infections and 37–87 deaths over 3 years and saved $30.5–$69.1 million, compared with no CRE control measures. When LTACHs and intensive care units intervened, prevalence decreased by a relative 21.2%. Adding LTACHs averted an additional 1,995 carriers, 513 infections, and 62 deaths, and saved $47.6 million beyond implementation in intensive care units alone. Thus, LTACHs may be more important than other acute care settings for controlling CRE, and regional efforts to control drug-resistant organisms should start with LTACHs as a centerpiece.
Genetic studies of IgA nephropathy: what have we learned from GWAS

Primary IgA Nephropathy is the most common glomerulonephritis in the world. It is most common in Asian populations, followed by Caucasians, yet relatively infrequent amongst African populations. The striking difference in the prevalence of IgAN between world populations, together with the known familial aggregation of disease, suggests an inherited mechanism. Recently three Genome-wide association studies (GWAS) of IgAN have identified seven susceptibility loci, providing initial insight into the genetic architecture of this complex trait. While genetic studies of complex traits are challenging, applying new genetic techniques and methods of analysis, especially Next-Generation Sequencing, will push the genetic studies of IgAN forward. Primary IgA Nephropathy (IgAN) is the most common glomerulonephritis in the world, and is especially prevalent in Asia, where it accounts for up to 45% of primary glomerulonephritis. Additionally, IgAN is one of the most common causes of end-stage renal disease (ESRD), with 15–40% of patients progressing to ESRD [1]. There is strong epidemiological and now molecular evidence for involvement of genetic factors in the pathogenesis of the disease[2,3]. In an effort to identify the susceptibility loci involved in sporadic cases of IgAN, genome wide association studies (GWAS) have been undertaken. GWAS have heralded a breakthrough in understanding the genetic basis of many complex diseases, enabling the discovery of common disease-causing alleles that have only a small effect on disease phenotype.
PROTEIN COMPLEXES ’98 Molecular Genetics of the Caveolin Gene Family: Implications for Human Cancers, Diabetes, Alzheimer Disease, and Muscular Dystrophy

Department of Molecular Pharmacology and the Albert Einstein Cancer Center, Department of Developmental and Molecular Biology, Department of Medicine, and the Albert Einstein Cancer Center, and Department of Cell Biology, Albert Einstein College of Medicine, Bronx; Servizio Malattie-Neuromuscolari, University of Genoa, Gaslini Institute, Genoa; and Department of Neurosciences, The Lerner Research Institute, Cleveland Clinic Foundation, Cleveland
Further Strategies to Improve the Working Experience of Rural Doctors Dietary Pattern amongst Obese and Nonobese Children in National Capital Territory of Delhi: A Case Control Study

Dear Editor, Vallikunnu et al. have presented the results of an insightful study on the working experience of rural doctors in Kerala. [1] A number of concerns were identified – these included concerns with regard to time, administrative and management work, professional development, and future prospects. All these issues are clearly important; however, it would also have been interesting to hear of the rural GPs’ views on other topics such as the role of teams in rural and remote healthcare, the relationship between primary care and secondary care in rural and remote healthcare, and the professional status of rural GPs. These are just some of the plethora of factors that affect working experience in rural and remote healthcare.
Beyond simple dichotomies in reinforcement learning.

Reinforcement learning (RL) is a framework of particular importance to psychology, neuroscience, and machine learning. Interactions between these fields, as promoted through the common hub of RL, has facilitated paradigm shifts relating multiple levels of analysis within a singular framework (e.g dopamine function). Recently, more sophisticated RL algorithms have been incorporated to better account for human learning, and in particular its oft documented reliance on two separable systems. However, along with many benefits, this dichotomous lens can distort questions, and may contribute to an unnecessarily narrow perspective on learning and decision making. Here we outline some of the consequences that come from over-confidently mapping algorithms, such as model-based vs. model-free RL, with putative cognitive processes. We argue that the field is well positioned to move beyond simplistic dichotomies, and we propose a means of re-focusing research questions toward the rich and complex components that comprise learning and decision making.
Prefrontal-Striatal Functional Pathology is Associated with Alcohol Abstinence Days at Treatment Initiation and Heavy Drinking After Treatment Initiation

Objective: Alcohol use disorders (AUDs) are associated with neuroadaptations in brain stress and reward circuits. It is not known whether such neuroadaptations are affected by alcohol abstinence days and also influence heavy drinking during the early treatment phase. A novel Functional Magnetic Resonance Imaging (fMRI) approach was utilized to assess brain responses during sustained exposure to standardized visual stimuli of stressful, alcohol cue and control, neutral images combined with prospective assessment of drinking outcomes during early outpatient treatment. Methods: In study 1, 44 treatment entering AUD patients and 43 demographically matched healthy controls (HC) participated in the fMRI experiment to identify dysfunctional responses associated with chronic alcohol abuse. In study 2, 69 AUD patients entering treatment assessed for whether fMRI responses at treatment initiation were influenced by alcohol abstinence and were prospectively predictive of early heavy drinking outcomes. Results: AUD patients, relative to HC showed hyperreactivity in the Ventro-medial Prefrontal Cortex (VmPFC) to neutral images, but VmPFC and ventral striatum hypoactivation to stress, and to alcohol cues relative to response to neutral images (whole brain, voxel based, p<.001, cluster corrected alpha=.05). In study 2, this specific prefrontal-ventral striatal dysfunction was associated with shorter days of alcohol abstinence (corr p<0.05), and also predicted greater number heavy drinking days during subsequent 2 weeks of treatment engagement (corr p<0.05). Conclusions: Alcohol abstinence days at treatment initiation significantly affects functional disruption of the prefrontal-striatal responses to stress and alcohol cues in AUD patients, and severity of this disruption, in turn, predicts greater heavy drinking during early treatment. Address correspondence to: Rajita Sinha, Ph.D., Yale University School of Medicine, Department of Psychiatry, Yale Stress Center, 2 Church Street South, Suite 209, New Haven, CT 06519. Rajita.Sinha@yale.edu. Drs. Blaine, Wemm, Fogelman, Scheinost, and Sinha, along with Ms. Lacadie report no financial relationships with commercial interests. HHS Public Access Author manuscript Am J Psychiatry. Author manuscript; available in PMC 2021 November 01. Published in final edited form as: Am J Psychiatry. 2020 November 01; 177(11): 1048–1059. doi:10.1176/appi.ajp. 2020.19070703. A uhor M anscript
Women A Model of Community Mobilization for the Prevention of HIV in Women and Infants

Ms. Person is a Behavioral Scientist with the Centers for Disease Control and Prevention, National Center for HIV, STD, and TB Prevention, Division of STD Prevention, Behavioral and Prevention Research Branch. Dr. Cotton is with Macro International, Inc. The Principal Investigators from the Prevention ofHIV in Women and Infants Demonstration Projects are Janet Adams, DrPH, Family Health Council, Inc., Pittsburgh, PA; Michael Stark, PhD, Multnomah County Health Department and Oregon Health Division, Portland, OR; Jennifer Lauby, PhD, Philadelphia Health Management Corporation, Philadelphia, PA; Patricia Evans, MD, MPH, Alameda County Health Care Services Agency, Oakland, CA; and Nancy Padian, PhD, University of California at San Francisco, San Francisco, CA. in Women and Infants