cssi/SciSciGPT-SciSciNet huggingface dataset:
Replication Stress Induces Genome-Wide Copy Number Changes in Human Cells That Resemble Polymorphic and Pathogenic Variants

Copy number variants (CNVs) are an important component of genomic variation in humans and other mammals. Similar de novo deletions and duplications, or copy number changes (CNCs), are now known to be a major cause of genetic and developmental disorders and to arise somatically in many cancers. A major mechanism leading to both CNVs and disease-associated CNCs is meiotic unequal crossing over, or nonallelic homologous recombination (NAHR), mediated by flanking repeated sequences or segmental duplications. Others appear to involve nonhomologous end joining (NHEJ) or aberrant replication suggesting a mitotic cell origin. Here we show that aphidicolin-induced replication stress in normal human cells leads to a high frequency of CNCs of tens to thousands of kilobases across the human genome that closely resemble CNVs and disease-associated CNCs. Most deletion and duplication breakpoint junctions were characterized by short (<6 bp) microhomologies, consistent with the hypothesis that these rearrangements were formed by NHEJ or a replication-coupled process, such as template switching. This is a previously unrecognized consequence of replication stress and suggests that replication fork stalling and subsequent error-prone repair are important mechanisms in the formation of CNVs and pathogenic CNCs in humans.
Effect of Alterations in Vasomotor Tone on Pressure-Flow Relationships in the Totally Perfused Dog

The technic of total body perfusion with a pump oxygenator system has been used to extend pressure flow studies to the circulation as a whole. The effect of alterations in vasomotor tone on both total peripheral resistance and pressure flow relationships has been investigated by surgical ablation of the central nervous system or administration of vasoactive drugs. Certain aspects of the results obtained are discussed in relation to the concept of critical closing pressures.
Toward an easy programming environment for implementing mobile applications: a fleet application case study using SyD middleware

This paper describes the advantages of SyD (System on Mobile Devices), a middleware technology for mobile devices and e-services, in terms of technology and programming. Features of SyD are illustrated here through our prototype application, a complex communication system for a trucking fleet that operates an automated package delivery system. The fleet system has been implemented in three ways, with SOAP, with JDBC, and with SyD. Our implementation experience shows that SyD greatly simplifies coding by allowing heterogeneous devices, peer-to-peer communications, group transactions based on triggering events, and mobility support through proxies and directory service.
Carbon monoxide diffusing capacity and mortality in pulmonary arterial hypertension

Background Abnormal carbon monoxide diffusing capacity (DLCO) is a marker of pulmonary vascular disease and predicts the presence of pulmonary arterial hypertension (PAH) and poor prognosis in diseases such as systemic sclerosis and idiopathic pulmonary fibrosis. Little is known of its prognostic utility in World Health Organization (WHO) Group I PAH. Methods We performed a cohort study of 408 patients with WHO Group I PAH from 1982 to 2006, with data on demographics, comorbidities, medications, functional class, laboratory tests, exercise testing, and hemodynamics. DLCO was determined upon entry into the study. We divided the cohort into tertiles based on DLCO and compared differences between groups. We used a Cox proportional hazards analysis to determine the association of DLCO with mortality, after adjusting for age, connective tissue disease etiology, functional class, pulmonary function testing variables, serum creatinine, albumin, hemoglobin, lung parenchymal abnormalities on chest computed tomography, oxygen use, and hemodynamic variables. Results The lowest tertile of DLCO was independently associated with an increased risk of death (univariate hazard ratio [HR] = 2.7, 95% confidence interval [CI] 1.9 to 3.9, p p = 0.025). On receiving operator characteristic (ROC) curve analysis, the c -statistic for the multivariate model without DLCO was 0.75, whereas the c -statistic for the multivariate model with DLCO was 0.78 ( p = 0.003 by likelihood ratio test). Importantly, a multivariate model with hemodynamic variables alone ( c -statistic = 0.61) was quite inferior to the multivariate model, which included DLCO. Conclusion DLCO is an independent predictor of death in patients with WHO Group I PAH.
Urinary IgA in IgA nephropathy and Henoch-Schoenlein purpura.

To determine the concentrations and molecular forms of urinary IgA in IgA nephropathy and Henoch-Schoenlein purpura, we studied 29 patients with these IgA-associated renal diseases (IgAN). Control groups comprised 10 patients with other diverse renal diseases and 11 healthy volunteers. Urinary IgA and IgG concentrations were higher in IgAN than in either control group and correlated positively with the serum creatinine concentration as well as the urinary protein excretion (P<0.01). However, IgA/IgG ratios did not differ among the three groups. Polymeric IgA (p-IgA) in the urine predominated only in normals; in IgAN and patients with other renal diseases, monomeric IgA (m-IgA) occurred almost exclusively. Serum IgA concentrations were generally normal in IgAN; four patients had concentrations greater than 500 mg/dl. Although the fraction of p-IgA in serum (median, 18%) was increased above normal (5–10%) in 13 of 16 (81%) subjects, neither the concentration of IgA or IgG nor the amount of p-IgA correlated with the serum creatinine concentration. These data suggest that the molecular form and concentration of urinary IgA are not discriminating for IgAN and are independent of these characteristics of serum IgA.
A comparative study of primary and immortalized cell adhesion characteristics to modified polymer surfaces: toward the goal of effective re-epithelialization.

Facilitating tissue regeneration or replacement requires development of synthetic surfaces that promote cell adhesion, migration, and proliferation. Two successful approaches have been to incorporate minimal cell adhesion recognition sequences at the biomaterial surface and to integrate the entire adhesion molecule into a compatible synthetic matrix. While adhesion assays using immortalized cell lines are important in evaluating synthetic materials, cell type and source play a significant role in the ability of such models to mimic real tissues. Models that utilize multiple cell types or primary cells are more representative of native tissues than models that use single cell types or primary cells. In this study we investigated primary respiratory epithelial cell (REC) adhesion to modified fluoropolymers incorporating simple functional groups and minimal peptide recognition sequences, and we evaluated the potential of hybrid biopolymer materials to support adhesion and proliferation. X-ray photoelectron spectroscopy (XPS) was used to verify substrate surface composition. Significant differences were found in the adhesion characteristics of primary REC and in the A549 lung carcinoma cell line. Model systems composed of multiple cell types and/or primary cells necessarily represent increased levels of complexity for an investigation of cellular responses to synthetic surfaces. When evaluating biomaterials, adhesion studies using immortalized cell lines cannot necessarily be extrapolated to normal cell behavior.
Pharmacoeconomic implications of thromboprophylaxis with new oral anticoagulants after total hip or knee replacement in the USA.

Introduction: Adequate thromboprophylaxis after total hip or knee replacement (THR or TKR) is essential to reduce the incidence of venous thromboembolism (VTE) and its associated complications. Although effective, traditional anticoagulants are associated with a considerable economic burden, particularly when used outside the hospital setting. This article explores whether newer oral anticoagulants can reduce costs of VTE prophylaxis and therapy. Areas covered: Cost associated with vitamin K antagonists; indirect costs associated with complicated or inconvenient anticoagulation regimens, non-adherence and associated complications; potential of the newer oral anticoagulants, including direct thrombin inhibitors and direct factor Xa inhibitors, to produce indirect cost savings after THR or TKR through a potential reduction in VTE rates and administration and monitoring costs. Expert opinion: The use of new anticoagulants for VTE prophylaxis after THR or TKR can result in direct and indirect cost savings thr...
Catalytic dehydrogenation of 1,2- and 1,3-diols

Abstract Described are studies of the dehydrogenation of 1,2- and 1,3-diols in homogenous solutions catalyzed by {[2,5-diphenyl-3,4-ditoluyl-(η5-C4CO)]2H}Ru2(CO)4(μ-H) (otherwise known as the Casey/Shvo catalyst). Both in the presence and absence of a dihydrogen acceptor, these reactions led to the analogous α-hydroxyketone as the only organic product. Isotopic labeling studies indicate that this product arises from reversible dehydrogenation/hydrogenation reactions, resulting in formation of the thermodynamically favored α-hydroxyketone. When this catalytic dehydrogenation was carried out in the presence of the rhodium decarbonylation catalyst Rh(dppp)2Cl (dppp = 1,3-bis(diphenylphosphino)propane), modest amounts of carbon monoxide result, suggesting that the dehydrogenation does generate at least some aldehydes that are intercepted by this catalyst. However, the efficiency of the latter reaction is poor.
Aspiration thrombectomy in a case of acute myocardial infarction due to coronary emboli in a patient with peripartum cardiomyopathy and mural thrombus

Acute coronary syndrome (ACS) due to embolic phenomenon in the setting of peripartum cardiomyopathy (PPCM) and left ventricular mural thrombus is a rare occurrence. There have been two known cases described in medical literature. We present a unique case in which catheter-based aspiration thrombectomy was used to successfully treat a patient with ACS due to coronary emboli in the setting of PPCMand left ventricular mural thrombus. We believe this to be the first report of the use of aspiration thrombectomy in such a clinical case.
Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks

DNA double-strand breaks (DSBs) are known to be powerful inducers of homologous recombination (HR), but single-strand breaks (nicks) have also been shown to trigger HR. Both DSB- and nick-induced HR ((nick)HR) are exploited in advanced genome-engineering approaches based on the bacterial RNA-guided nuclease Cas9. However, the mechanisms of (nick)HR are largely unexplored. Here, we applied Cas9 nickases to study (nick)HR in mammalian cells. We find that (nick)HR is unaffected by inhibition of major damage signaling kinases and that it is not suppressed by nonhomologous end-joining (NHEJ) components, arguing that nick processing does not require a DSB intermediate to trigger HR. Relative to a single nick, nicking both strands enhances HR, consistent with a DSB intermediate, even when nicks are induced up to ∼1kb apart. Accordingly, HR and NHEJ compete for repair of these paired nicks, but, surprisingly, only when 5' overhangs or blunt ends can be generated. Our study advances the understanding of molecular mechanisms driving nick and paired-nick repair in mammalian cells and clarify phenomena associated with Cas9-mediated genome editing.
Online feasibility study about HIV-negative male couples substance use with weekly ecological momentary diary assessments

s / Drug and Alcohol Dependence 156 (2015) e102–e182 e153 Online feasibility study about HIV-negative male couples substance use with weekly ecological momentary diary assessments Jason W. Mitchell 1, Francesca Davis1, Yue Pan2, Daniel J. Feaster1 1 Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, United States 2 University of Miami Miller School of Medicine, Miami, FL, United States Aims: To date, little is known about male couples’ use of substances despite the role that substance use plays in HIV seroconversion among gay men. The aims of the present study were twofold: (1) to assess whether panel dyadic data could be collected from HIV-negative male couples about their substance use using online weekly ecological momentary diary assessments; (2) to examine couples’ rates of substance use and contexts of their usage. Methods: A longitudinal study design using ecological momentary weekly electronic diaries was used to examine male couples substance use with/out sex, and the contexts of their usage over a 6-week period. Targeted facebook ads were used to recruit the sample along with a partner referral system to invite eligible participants’ main partners. 531 men took the screener; of these, 97 were eligible, consented and enrolled in the study. Results:Although97partneredmenenrolled, only 13male couples with both partners and 15 male couples with one partner participated in the study. Over the 6-week period, men’s engagement inUASwith theirmain partner, alcohol consumption, and use of erectile dysfunction medication, prescription pain medication (PPM), and/or illicit drug(s) varied. Men frequently usedmarijuana and/or alcohol in a variety of contexts including sex. Among the 13 male couples, both partner’s use of illicit drugs includingmarijuana (ICC 0.97, P 5 posts for analysis. Results: Qualitative analysis of individual posts indicated that Internet discussionparticipants emphasized the therapeutic effects of cannabis for ADHD – fewer endorsed either a null or harmful impact. Exploratory analysis also indicated that participants perceived fewer concerns about cannabis due to it being “natural,” that cannabis is perceived to improve impairment in ADHD (e.g., driving), distrust of the medical community regarding stimulant medication efficacy, and a preference for particular cannabis strains. Conclusions: Cannabis use in the US is changing and there is a need for further research of how cannabis impacts at-risk groups, such as those with ADHD. This qualitative study provides new insight into currentlyheldperceptions about cannabisuse inADHD. We propose a number of novel hypotheses guided by qualitative analysis ofweb-forumcontent,which canguide future quantitative
Sunlight as an energetic driver in the synthesis of molecules necessary for life

Solar radiation was overwhelmingly the largest source of energy on the early Earth. Energy provided by the Sun has the potential to access different chemistries than energy provided by other sources, such as hydrothermal vents, because of the unique characteristics of photochemistry that differentiate it from conventional thermal chemistry. This review considers how sunlight-driven reactions can abiotically generate prebiotic molecules necessary for the evolution of life. We discuss briefly the characteristics of the early Sun and the likely environmental conditions on the early Earth because photochemistry is both environment- and molecule-specific. An overview of the fundamental principles of photophysics and photochemistry is followed by discussion of a selection of prebiotically-relevant examples of photochemical reactions, focusing on syntheses that lead to the production of cellular components (e.g. sugars, lipids, and biopolymer precursors). The role of photostability as an evolutionary driving force is also considered. These examples highlight the ability of simple organic molecules to harness solar energy and convert it into high-energy chemical bonds, generating molecular complexity.
Familial aggregation of subcutaneous fat deposits and the peripheral fat distribution pattern

The familial aggregation of fatness into subcutaneous fat distribution was studied in a sample of 122 nuclear families with adolescent children. Subcutaneous fat thickness was measured using ultrasound images. Other variables considered were anthropometric measurements, body composition, and indices of relative fat distribution. The measurements were adjusted for age and body mass index (BMI), and the residuals were transformed to normalized z-scores by sex and age group. The z-scores were used to calculated intraclass correlations between all family members. The results show significant familial correlations for the fat deposits on the upper abdomen, triceps, calf, and subscapula. They also show strong familial aggregation for the level of fatness and ponderosity. However, the subcutaneous fat on the lower abdomen and the corresponding indices were closely related to the level of fatness, and were significantly correlated between sisters, and between mothers and daughters. These lower abdominal fat deposits are more likely to be influenced by environmental components such as diet and level of physical activity.
The long reach of lean retailing: Firm embeddedness and Wal-Mart’s implementation of local produce sourcing in the US:

With its corresponding concepts of societal, territorial, and network embeddedness, firm embeddedness offers a theoretical framework for analyzing how retailers develop strategies and business mode...
Bioturbation-influenced fluid pathways within a carbonate platform system: The Lower Cretaceous (Aptian–Albian) Glen Rose Limestone

Abstract The Aptian–Albian Glen Rose Limestone (GRL) is an argillaceous shallow-marine carbonate deposit on the Central Texas Platform and contains the upper Trinity aquifer and the upper part of the middle Trinity aquifer. The GRL is divided into Upper and Lower GRL members, which have been further subdivided into hydrostratigraphic units (HSUs). This study uses an integrated ichnological and sedimentological approach to record changes in ichnofabric index (ii) as a proxy for bioturbation within the GRL and relates these changes to fluid flow. Fluid pathways within HSUs are controlled by the complex interaction of faults and fractures, karst development, and large-scale bioturbation-influenced porosity and permeability. The effect of bioturbation-influenced porosity as an aquifer characteristic is the least studied of these factors. Post-depositional solution enhancement of ichnofossils is also common and has increased lateral and vertical fluid connectivity in some HSUs. Most GRL strata are dominated by Thalassinoides networks, but also contain Palaeophycus, Planolites, Ophiomorpha, Serpulid worm tubes, rhizoliths, and Cruziana. Thalassinoides are commonly filled with coarser sediment than the surrounding matrix and act as fluid conduits within an otherwise low permeability matrix. Beds with ii3–4 and burrows with permeable fill transmit water readily. Beds with ii5–6 are commonly muddy and heavily homogenized, restricting fluid flow. Grainstone beds commonly have ii1–2 and are well cemented, restricting fluid flow to low intergranular flow. Pore systems dominated by Thalassinoides ichnofabrics, such as the GRL, are difficult to characterize on a large scale using many laboratory methods because they create heterogeneous flow paths depending on difference in permeability between the matrix and burrow fill. Understanding the effects of bioturbation-influenced porosity and permeability on subsurface fluid pathways is vital for creating a geologic and hydrostratigraphic framework for the Trinity aquifer.
Analysis of managed aquifer recharge for retiming streamflow in an alluvial river

Abstract Maintenance of low flows during dry periods is critical for supporting ecosystem function in many rivers. Managed aquifer recharge is one method that can be used to augment low flows in rivers that are hydraulically connected to an alluvial groundwater system. In this study, we performed numerical modeling to evaluate a managed recharge operation designed to retime streamflow in the South Platte River, northeastern Colorado (USA). Modeling involved the simulation of spatially and temporally variable groundwater-surface water exchange, as well as streamflow routing in the river. Periodic solutions that incorporate seasonality were developed for two scenarios, a natural base case scenario and an active management scenario that included groundwater pumping and managed recharge. A framework was developed to compare the scenarios by analyzing changes in head-dependent inflows and outflows to/from the aquifer, which was used to interpret the simulated impacts on streamflow. The results clearly illustrate a retiming of streamflow. Groundwater pumping near the river during winter months causes a reduction in streamflow during those months. Delivery of the pumped water to recharge ponds, located further from the river, has the intended effect of augmenting streamflow during low-flow summer months. Higher streamflow is not limited to the target time period, however, which highlights an inefficiency of flow augmentation projects that rely on water retention in the subsurface.
Billion dollar boreal woodland caribou and the biodiversity impacts of the global oil and gas industry

Abstract Awareness of the impact of the global energy industry and associated landuse change on biodiversity conservation has been steadily growing amongst conservation biologists. Across Canada, 28 of 57 populations of boreal woodland caribou ( Rangifer tarandus caribou) are declining and 20 of 25 southern mountain populations are in decline with several recent high-profile extirpations. Declines stem from widespread landuse change from energy development and forestry that will take decades to recover, if ever. In Western Canada's Boreal forest, a globally significant oil and gas industry has emerged that is the biggest source of foreign oil to US markets. All woodland caribou populations overlapping oil and gas development in oil-rich Alberta are in rapid decline, shrinking by 50% every 8 years. After a decade of delay, the Federal government released recovery plans under the Canadian Species-at-Risk Act (SARA) in 2012 and 2014 for these two caribou ecotypes, and will audit provincial compliance in 2017. Yet recovery actions have been inadequate, and have relied on wolf control as a short-term solution. Given the stark reality, conservation triage might be expected. Instead, the conservation objective at Federal and Provincial levels remains legally committed to recovery of all populations despite the paradox of continued declines. I suggest the reason for ineffective conservation planning is the staggering cost of effective habitat protection that far exceeds $150 billion (CDN) in Alberta alone. Declines of woodland caribou also allegedly violate Canadian Aboriginal treaty rights that have been challenged in court. This complex conservation case-study urgently illustrates the need for strategic conservation triage at provincial and national levels. And more generally, caribou conservation demonstrates the challenge of using national endangered species legislation to retroactively counteract the global energy industry without strategic conservation planning coordinated with energy and cultural policies.
Knowledge for Natural Disasters

Just as the rich knowledge of craftsmen was once the basis of working life, the complex knowledge of ordinary people has organized life outside of work and held communities together to confront all kinds of disasters. In this paper, FEMA’s model of man prevented it from understanding how local knowledge could be used to prepare for an earthquake and then contributed to making things worse in New Orleans. This paper explores the use of another model of socially distributed knowledge and action for protecting people from natural disasters, especially at the bottom.
Constructing compact causal mathematical models for complex dynamics

From microbial communities, human physiology to social and bio- logical/neural networks, complex interdependent systems display multi-scale spatio-temporal pa erns that are frequently classi ed as non-linear, non-Gaussian, non-ergodic, and/or fractal. Distin- guishing between the sources of nonlinearity, identifying the na- ture of fractality (space versus time) and encapsulating the non- Gaussian characteristics into dynamic causal models remains a ma- jor challenge for studying complex systems. In this paper, we pro- pose a new mathematical strategy for constructing compact yet ac- curate models of complex systems dynamics that aim to scrutinize the causal e ects and in uences by analyzing the statistics of the magnitude increments and the inter-event times of stochastic pro- cesses. We derive a framework that enables to incorporate knowl- edge about the causal dynamics of the magnitude increments and the inter-event times of stochastic processes into a multi-fractional order nonlinear partial di erential equation for the probability to nd the system in a speci c state at one time. Rather than follow- ing the current trends in nonlinear system modeling which pos- tulate speci c mathematical expressions, this mathematical frame- work enables us to connect the microscopic dependencies between the magnitude increments and the inter-event times of one stochas- tic process to other processes and justify the degree of nonlinearity. In addition, the newly presented formalism allows to investigate appropriateness of using multi-fractional order dynamical models for various complex system which was overlooked in the literature. We run extensive experiments on several sets of physiological pro- cesses and demonstrate that the derived mathematical models o er superior accuracy over state of the art techniques.
How to Really Make America Great Again: Lessons About Selflessness from the Book of Ruth

America is in crisis and appears to have lost its moral compass. People have little confidence in its institutions ranging from Congress to the Presidency. This paper examines the Book of Ruth and shows that there are many powerful lessons for our society contained in it. One key lesson is the importance of selfless, altruistic kindness, especially on the part of leaders. It also has a powerful message about xenophobia. Other lessons that can be derived from this story are discussed.
B-Cell Therapies in Multiple Sclerosis

B cells play a vital function in multiple sclerosis (MS) pathogenesis through an array of effector functions. All currently approved MS disease-modifying therapies alter the frequency, phenotype, or homing of B cells in one way or another. The importance of this mechanism of action has been reinforced with the successful development and clinical testing of B-cell-depleting monoclonal antibodies that target the CD20 surface antigen. Ocrelizumab, a humanized anti-CD20 monoclonal antibody, was approved by the Food and Drug Administration (FDA) in March 2017 after pivotal trials showed dramatic reductions in inflammatory disease activity in relapsing MS as well as lessening of disability progression in primary progressive MS. These and other clinical studies place B cells at the center of the inflammatory cascade in MS and provide a launching point for development of therapies that target selective pathogenic B-cell populations.
A general model for multiple view unsupervised learning

Multiple view data, which have multiple representations from different feature spaces or graph spaces, arise in various data mining applications such as information retrieval, bioinformatics and social network analysis. Since different representations could have very different statistical properties, how to learn a consensus pattern from multiple representations is a challenging problem. In this paper, we propose a general model for multiple view unsupervised learning. The proposed model introduces the concept of mapping function to make the different patterns from different pattern spaces comparable and hence an optimal pattern can be learned from the multiple patterns of multiple representations. Under this model, we formulate two specific models for two important cases of unsupervised learning, clustering and spectral dimensionality reduction; we derive an iterating algorithm for multiple view clustering, and a simple algorithm providing a global optimum to multiple spectral dimensionality reduction. We also extend the proposed model and algorithms to evolutionary clustering and unsupervised learning with side information. Empirical evaluations on both synthetic and real data sets demonstrate the effectiveness of the proposed model and algorithms.
Conclusion and Synthesis

Figure 16-1 shows the biomass and production pyramids for the Lake Lanao plankton system plus the transfer efficiencies between trophic levels. Transfer efficiency between the solar source and the phytoplankton community is relatively high in view of the low nutrient base in Lake Lanao. The summary of IBP data given by Brylinsky and Mann (1973) shows an average value of 0.4% for transfer of photosynthetically available solar energy (PAR, ca. 350–700 nm) to gross production. In terms of net production, which is of more interest here, this would be 0.2 to 0.3% based on PAR or about 0.1 to 0.15 based on total solar radiation. The percentage reported in Figure 9-1, which is based on total radiation, is obviously quite high. Efficient nutrient cycling by the mechanisms described in Chapter 3 is in large part responsible for minimization of severe nutrient depletion and consequent maintenance of high transfer efficiency at the first trophic level (Lewis, 1974).
O tipping point: usando o discurso diagnóstico de pacientes simulados para educar intérpretes médicos

Rather than amassing 10,000 hours of practice before mastery is achieved – Ericsson’s famed tipping point – medical interpreters can gain considerable, concomitant experience by analyzing videos of provider-patient interactions, even when the pair speak the same language. Teaching hospitals commonly film such interactions using standardized patients (SPs). Such films have been effectively used in classroom-based instruction with interpreters. The novel use of SP films in an on-line learning environment is described herein, where discussion boards and worksheets supplanted traditional instruction methods. In this problem-based learning (PBL) approach, typical of medical education, graduate-level medical interpreting students became familiar with common diagnostic and treatment discourse. Students reported that this familiarity helped free their cognitive resources for planning and monitoring translations and other decisions on-the-job. The learning materials and methods used in this on-line approach are detailed. The value of the PBL context is described in relation to healthcare interpreting education approaches generally.
Two New Heuristic Methods for Protein Model Quality Assessment

Protein tertiary structure prediction is an important open challenge in bioinformatics and requires effective methods to accurately evaluate the quality of protein 3-D models generated computationally. Many quality assessment (QA) methods have been proposed over the past three decades. However, the accuracy or robustness is unsatisfactory for practical applications. In this paper, two new heuristic QA methods are proposed: MUfoldQA_S and MUfoldQA_C. The MUfoldQA_S is a quasi-single-model QA method that assesses the model quality based on the known protein structures with similar sequences. This algorithm can be directly applied to protein fragments without the necessity of building a full structural model. A BLOSUM-based heuristic is also introduced to help differentiate accurate templates from poor ones. In MUfoldQA_C, the ideas from MUfoldQA_S were combined with the consensus approach to create a multi-model QA method that could also utilize information from existing reference models and have demonstrated improved performance. Extensive experimental results of these two methods have shown significant improvement over existing methods. In addition, both methods have been blindly tested in the CASP12 world-wide competition in the protein structure prediction field and ranked as top performers in their respective categories.
Diagnostic thresholds for pregnancy hyperglycemia, maternal weight status and the risk of childhood obesity in a diverse Northern California cohort using health care delivery system data.

Objective To estimate the risk of childhood obesity associated with the various criteria proposed for diagnosis of gestational diabetes (GDM), and the joint effects with maternal BMI. Methods Cohort study of 46,396 women delivering at the Kaiser Permanente Northern California health care delivery system in 1995–2004 and their offspring, followed through 5–7 years of age. Pregnancy hyperglycemia was categorized according to the screening and oral glucose tolerance test values proposed for the diagnosis of GDM by the International Association of the Diabetes and Pregnancy Study Group (IADPSG), Carpenter Coustan (CC), and the National Diabetes Data Group (NDDG). Childhood obesity was defined by the International Obesity Task Force’s age and sex-specific BMI cut-offs. Poisson regression models estimated the risks of childhood obesity associated with each category of pregnancy glycemia compared to normal screening, and the joint effects of maternal BMI category and GDM by the CC and the IADPSG criteria. Results Compared with normal screening, increased risks of childhood obesity were observed for abnormal screening [RR (95% CI): 1.30 (1.22, 1.38)], 1+ abnormal values by the IADPSG or CC [1.47 (1.36, 1.59) and 1.48 (1.37, 1.59), respectively], and 2+ values by CC or NDDG [1.52 (1.39, 1.67) and 1.60 (1.43, 1.78), respectively]. Compared to obese women without GDM, obese women with GDM defined by the CC criteria had significantly increased risk of childhood obesity [1.20 (1.07, 1.34)], which was also observed for GDM by the IADSPG [1.18 (1.07, 1.30)], though GDM did not significantly increase the risk of childhood obesity among normal weight or overweight women. Conclusions The risk of childhood obesity starts to increase at levels of pregnancy glycemia below those used to diagnose GDM and the effect of GDM on childhood obesity risk appears more pronounced in women with obesity. Interventions to reduce obesity and pregnancy hyperglycemia are warranted.
Sorcery and Sovereignty: Bodin’s Political Economy of the Occult

While much has been written on Six Books on the Commonwealth and his Demonmania, scholarship on Jean Bodin generally treats these as two separate areas of inquiry. Moreover, discussions of Bodin’s ...
Legal and Economic Reglamentation Aspects of Individual Enterprise Functioning

The operation of individual enterprises established in Lithuania was regulated by various separate laws which caused much inconvenience. Therefore, the Lithuanian law on individual enterprises entered into force on 1 January 2004. The article aims to present the outstanding peculiarities of an individual enterprise as a legal entity which could be considered as advantages and disadvantages. The article considers the individual enterprise before and after the entry into force of the Lithuanian law on individual enterprises.
Copyright Education for Graduate Students: A Multi-Stage Approach

INTRODUCTION This article illustrates how academic librarians can structure a copyright education program for graduate students according to models of graduate student persistence. Adapting copyright education to stages of graduate persistence can help academic librarians find ways to strategically allocate resources while best educating students. DESCRIPTION OF PROGRAM The article examines how students at the transition, development, and research stages of their education are served by differing types of copyright education such as tutorials, workshops, and consultations. At the large research library where the authors implemented this model, the multi-staged structure of the program allowed librarians to educate students about a broad array of copyright topics throughout their graduate programs instead of addressing issues solely related to dissertations and theses at the end of their studies. Implementing this model of copyright education for graduate students has implications for program scale, instruction across disciplines, and the reduction of graduate student anxiety. NEXT STEPS This program is subject to iterative improvements, and in the future the authors would like to expand early-stage graduate programming and investigate graduate student perceptions of copyright education.
Post Pulmonary Thromboendarterectomy Atrial Arrhythmias and Impact on Length of Stay

Background Post-operative atrial arrhythmias (POAA) after cardiac surgery are common and known to prolong hospital length of stay (LOS), but have been reported grouping atrial fibrillation (POAF), atrial flutters (AFL), and atrial tachycardias (AT). The impact of POAA vs. specifically POAF on intensive care unit time (ICUT) and hospital LOS after pulmonary thromboendarterectomy surgery (PTE) remains unknown. Objective To determine the impact of POAA and POAF on ICUT and hospital LOS after PTE. Method We identified consecutive patients undergoing PTE at our medical center from June 2013 to March 2020. After assessing baseline patient characteristics, we compared ICUT and LOS in patients with and without POAA and POAF after PTE. Results A total of 224 patients underwent PTE. POAA occurred in 31% (n = 68), of which 71% (n = 48) were POAF. Patients who developed POAA were older on average (63.5 vs. 51.5 years, p Conclusion In an adjusted analysis, in patients undergoing PTE, neither development of POAA nor specifically POAF were associated with increased ICUT. However, both POAA and POAF were associated with longer hospital LOS, denoting that POAA and POAF prolong hospitalization outside the ICU.
Exact Coupling of Random Walks on Polish Groups

Exact coupling of random walks is studied. Conditions for admitting a successful exact coupling are given that are necessary and in the Abelian case also sufficient. In the Abelian case, it is shown that a random walk S with step-length distribution $$\mu $$ started at 0 admits a successful exact coupling with a version $$S^x$$ started at x if and only if there is $$n\geqslant 1$$ with $$\mu ^{n} \wedge \mu ^{n}(x+\cdot ) \ne 0$$ . Moreover, when a successful exact coupling exists, the total variation distance between $$S_n$$ and $$S^x_n$$ is determined to be $$O(n^{-1/2})$$ if x has infinite order, or $$O(\rho ^n)$$ for some $$\rho \in (0,1)$$ if x has finite order. In particular, this paper solves a problem posed by H. Thorisson on successful exact coupling of random walks on $${\mathbb {R}}$$ . It is also noted that the set of such x for which a successful exact coupling can be constructed is a Borel measurable group. Lastly, the weaker notion of possible exact coupling and its relationship to successful exact coupling are studied.
Surface structuring comparison for multiple glasses using a pulsed CO2 laser

Fabrication of ridge and trench structures in soda lime, borosilicate and fused silica glasses using pulsed CO2 laser are demonstrated. Effects of laser power, stage temperature on dimensions and quality of structures is discussed.
Complexities and opportunities in teachers' generation of videos from their own classrooms

Abstract Video cameras have become smaller and increasingly embedded in our social lives. This study investigates the implications of these changes for teachers' work with video in professional development. Specifically, we focus on complexities and opportunities associated with teachers generating videos from their own classrooms, in the context of a short online course where teachers tried several mathematical activities that invited student reasoning and discussion. We unpack the potential affordances of video generation for teacher learning by examining teachers' processes — how they captured video during instruction and selected clips to share — and the characteristics of their final video products. Analyses demonstrated that generating video clips was complex work for teachers, requiring coordination of multiple sets of considerations about their students, the video itself, video viewers, and the course. Further, capturing and selecting sparked different emphases for teachers. While capturing, teachers foregrounded video quality considerations while seeking to support students' experiences. Selecting engaged teachers in curating (and hence attending to) student thinking within their videos. Teachers' video products also demonstrated characteristics known to be supportive of teacher learning. We see these results as cause for optimism about the potential of teachers' video generation for supporting teacher learning.
Morphological Correlations in Nasolabial Formation After Primary Lip Repair for Unilateral Cleft Lip.

Purpose We aim to reveal postoperative morphological correlations between the nasolabial components in patients with unilateral cleft lip (UCL). The hypothetical correlations are first, a correlation between the vertical height of the cleft-side alar base and the length of the cleft-side red lip, and second, a correlation between the length of the cleft-side red lip and the vertical position of the cleft-side oral commissure. We explain how these morphological balances are controlled by surgery. Methods Three-dimensional bilateral measurements of the length of the red lip, vertical height of the nasal alar base, and vertical height of the oral commissure were conducted retrospectively on 31 patients with UCL and palate (complete UCL: 26; incomplete UCL: 5) who underwent primary lip plasty at Osaka Women's and Children's Hospital from 2017 to 2019. Results We found a statistically significant correlation between the vertical height of the cleft-side alar base and cleft-side red lip length (P = .012, r = 0.45); thus, the longer the red lip, the lower was the nasal alar base. The correlation between the cleft-side red lip length and the vertical height of the cleft-side oral commissure also showed a statistical significance (P = .00074, r = 0.57); thus, the shorter the red lip, the higher was the oral commissure. Conclusions The present results provided objective evidence showing basic morphological relationships between the postoperative nasolabial features of patients with UCL. The results lead to a reasonable approach to define the proposed peak of the Cupid's bow, an unsettled major controversy in cleft lip surgery.
Comunidades indígenas de Oaxaca, México. Problemas, oportunidades y retos en salud pública con atención especial en salud mental

Objetivos: Presentar un instrumento en Mixteco, Zapoteco, y Espanol para valorar la salud mental de las comunidades Indigenas de Oaxaca, Mexico. Proveer sugerencias sobre como este instrumento puede ser util para las comunidades indigenas de otras regiones de Latinoamerica. Metodos: Este manuscrito incluye una revision teorica de articulos publicados en el area de la salud mental de las comunidades originarias de Oaxaca, Mexico y presenta el proceso para el desarrollo de un instrumento de salud mental culturalmente apropiado. El instrumento fue creado por una enfermera de practica avanzada de habla Hispana y traducido por un estudiante universitario trabajador en salud publica y una enfermera profesional nativos de Oaxaca, Mexico y lingo-parlantes en Mixteco y Zapoteco. Resultados: Un instrumento culturalmente apropiado fue desarrollado para valorar la salud mental de las personas de origen Oaxaqueno. Este instrumento incluye algunas preguntas relacionadas con la Pandemia de Covid-19. Fue traducido en Espanol, Mixteco y Zapoteco. La version en Espanol esta disponible en la forma escrita pero las versiones en Mixteco y Zapoteco estan disponibles en forma de audio ya que son lenguas de tradicion oral. Conclusiones: Las necesidades de salud de las comunidades Oaxaquenas que viven en los Estados Unidos y en otras partes de Latinoamerica son apremiantes y mas aun en el area de la salud mental. El instrumento para valorar la salud mental de este grupo poblacional discutido aqui es una contribucion al entendimiento y la solucion de los problemas relevantes identificados.
Grow fast, die young: Does compensatory growth reduce survival of juvenile blacktip sharks (Carcharhinus limbatus) in the western Gulf of Mexico?

Effective conservation and management necessitate an understanding of the ecological mechanisms that shape species life histories in order to predict how variability in natural and anthropogenic impacts will alter growth rates, recruitment, and survival. Among these mechanisms, the interaction between parturition timing and prey availability frequently influences offspring success, particularly when postnatal care is absent. Here, we assess how parturition timing and nursery conditions, including prey abundance and environmental conditions, influence the growth and potential survival of blacktip sharks (Carcharhinus limbatus) in western Gulf of Mexico (GOM) estuaries over their first year. Catch data from long-term gillnet monitoring allowed for clear delineation of cohorts based on size frequency distribution plots, and showed that late parturition cohorts born in estuaries with fewer prey resources exhibited more rapid growth than early parturition cohorts that experienced more abundant prey. Compensatory behaviors that promoted accelerated growth led to reduced second year residency, likely due to reduced survival resultant from greater risk taking and potentially due to reduced site fidelity attributed to larger body size. Water temperatures influenced blacktip growth rates through physiological increases in metabolism and potential premigratory foraging cues associated with cooling temperatures. Gradual warming of the GOM (0.03°C year-1) was also correlated with earlier parturition across the study period (1982-2017), similar to other migratory species. Considering current trends in climate and associated phenological shifts in many animals, testing hypotheses assessing compensatory growth-risk trade-offs is important moving forward to predict changes in life histories and associated recruitment in concert with current and future conservation actions, like wildlife management.
Synaptic microRNAs Coordinately Regulate Synaptic mRNAs: Perturbation by Chronic Alcohol Consumption

Local translation of mRNAs in the synapse has a major role in synaptic structure and function. Chronic alcohol use causes persistent changes in synaptic mRNA expression, possibly mediated by microRNAs localized in the synapse. We profiled the transcriptome of synaptoneurosomes (SN) obtained from the amygdala of mice that consumed 20% ethanol (alcohol) in a 30-day continuous two-bottle choice test to identify the microRNAs that target alcohol-induced mRNAs. SN are membrane vesicles containing pre- and post-synaptic compartments of neurons and astroglia and are a unique model for studying the synaptic transcriptome. We previously showed that chronic alcohol regulates mRNA expression in a coordinated manner. Here, we examine microRNAs and mRNAs from the same samples to define alcohol-responsive synaptic microRNAs and their predicted interactions with targeted mRNAs. The aim of the study was to identify the microRNA-mRNA synaptic interactions that are altered by alcohol. This was accomplished by comparing the effect of alcohol in SN and total homogenate preparations from the same samples. We used a combination of unbiased bioinformatic methods (differential expression, correlation, co-expression, microRNA-mRNA target prediction, co-targeting, and cell type-specific analyses) to identify key alcohol-sensitive microRNAs. Prediction analysis showed that a subset of alcohol-responsive microRNAs was predicted to target many alcohol-responsive mRNAs, providing a bidirectional analysis for identifying microRNA-mRNA interactions. We found microRNAs and mRNAs with overlapping patterns of expression that correlated with alcohol consumption. Cell type-specific analysis revealed that a significant number of alcohol-responsive mRNAs and microRNAs were unique to glutamate neurons and were predicted to target each other. Chronic alcohol consumption appears to perturb the coordinated microRNA regulation of mRNAs in SN, a mechanism that may explain the aberrations in synaptic plasticity affecting the alcoholic brain.