Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is known about how decisions made during annotation affect the reliability of the results. Here, we use statistical simulations to rigorously assess how to optimize annotation accuracy and speed, given parameters of the input data like read length and library size. We identify best practices in metagenome annotation and use them to guide the development of the Shotgun Metagenome Annotation Pipeline (ShotMAP). ShotMAP is an analytically flexible, end-to-end annotation pipeline that can be implemented either on a local computer or a cloud compute cluster. We use ShotMAP to assess how different annotation databases impact the interpretation of how marine metagenome and metatranscriptome functional capacity changes across seasons. We also apply ShotMAP to data obtained from a clinical microbiome investigation of inflammatory bowel disease. This analysis finds that gut microbiota collected from Crohn’s disease patients are functionally distinct from gut microbiota collected from either ulcerative colitis patients or healthy controls, with differential abundance of metabolic pathways related to host-microbiome interactions that may serve as putative biomarkers of disease. Author Summary Microbial communities perform a wide variety of functions, from marine photosynthesis to aiding digestion in the human gut. Shotgun “metagenomic” sequencing can be used to sample millions of short DNA sequences from such communities directly, without needing to first culture its constituents in the laboratory. Using these data, researchers can survey which functions are encoded by mapping these short sequences to known protein families and pathways. Several tools for this annotation already exist. But, annotation is a multi-step process that includes identification of genes in a metagenome and determination of the type of protein each gene encodes. We currently know little about how different choices of parameters during annotation influences the final results. In this work, we systematically test how several key decisions affect the accuracy and speed of annotation, and based on these results, develop new software for annotation, which we named ShotMAP. We then use ShotMAP to functionally characterize marine communities and gut communities in a clinical cohort of inflammatory bowel disease. We find several functions are differentially represented in the gut microbiome of Crohn’s disease patients, which could be candidates for biomarkers and could also offer insight into the pathophysiology of Crohn’s. ShotMAP is freely available (https://github.com/sharpton/shotmap).
Impact of Empiric Antibiotic Use on Development of Infections caused by Extended-Spectrum β-Lactamase Bacteria in a Neonatal Intensive Care Unit

Background: The neonatal intensive care unit at Miller Children's Hospital changed from empiric use of cefotaxime and vancomycin (CEF) to tobramycin and vancomycin (TOB) for hospital-acquired infections in November 1999 because of an increase in infections caused by extended-spectrum β-lactamase (ESBL)-producing bacteria. The objectives of this study were to evaluate the incidence and impact of this change on the development of ESBL infections. Methods: We retrospectively reviewed medical records of infants who received CEF or TOB between January 1998 and December 2002. A standardized form was used to collect demographic data, information on antibiotic use, and culture results. Results: The mean gestational age and birth weight of the 250 infants were 28.8 ± 4.0 weeks and 1213.1 ± 662 g, respectively. There were no differences between infants who received CEF (N = 130) or TOB (N = 120) in terms of gestational age, birth weight, device use, invasive procedures, or prior antibiotic use. There were 11 ESBL infections. Infants in the CEF group were more likely than those in the TOB group to develop ESBL infection (7.8% versus 0.8%, P = 0.008). There were 11 deaths, with none attributed to ESBL infection. In a multivariate analysis, duration of prior ampicillin and gentamicin use and exposure to CEF were associated with ESBL infection [odds ratio (OR): 3.1, 95% confidence interval (CI): 1.28–7.49, P = 0.012; and OR: 33.7; 95% CI: 1.02–1136, P = 0.05, respectively]. Conclusions: The change from empiric use of CEF to TOB was associated with a significant decrease in the incidence of ESBL infections.
Histological and cytological study of the bed nuclei of the stria terminalis in adult rat. II. Oval nucleus: Extrinsic inputs, cell types, neuropil, and neuronal modules

The oval nucleus (Ov) of the bed nuclei of the stria terminalis was studied in adult rats. The Ov is composed of 11 neuron types distributed into a shell and a core domain. The stria terminalis, internal capsule, ventral amygdaloid pathway, and medial forebrain bundle are the main sources of afferents to the neuropil of the Ov. The nucleus shell contains abundant intrinsic neurons possibly connected among themselves and with the core by centripetal axon collaterals. Series of intrinsic neurons in the shell, linked with both short‐axon and projecting neurons in the core, suggest a centripetal control of projecting neurons. In situ hybidization for vesicular glutamate transporter (VGlu) and glutamic acid decarboxylase (GAD) show numerous GAD‐synthesizing neurons and an absence of VGlu‐synthesizing neurons. In the electron microscope, the neuropil of the Ov contains axospinous, axoshaft, axosomatic, mixed (i.e., chemical‐electrical), and axoaxonic synapses, in order of frequency. Synaptic boutons in apposition with the initial segment, represent an additional axoaxonic interaction. Further neural synchronization of the Ov occurs via gap junctions between somata, soma‐dendrite, and possibly by apposition between axon terminals. The putative inputs from the major tracts of the forebrain coupled with the cytological organization of the Ov make it one of the most complex structures of the mammalian brain. J. Comp. Neurol. 497:772–807, 2006. © 2006 Wiley‐Liss, Inc.
Locus of control, television viewing, and eating disorder symptomatology in young females.

The purpose of this study was to assess the effects of locus of control and television watching (number of hours of television watched per week) on eating disorder symptomatology in girls between the ages 10-17 years. A 2 x 2 factorial design was employed in which girls were identified either as (a) being higher or lower viewers of television, and (b) having either an external or internal locus of control. Girls with an external locus of control had significantly greater eating disorder symptomatology than those with an internal locus of control. For girls watching higher amounts of television, those having an external locus of control had significantly greater eating disorder symptomatology than those having an internal locus of control.
Diabetes mellitus with normal renal function is associated with anaemia

Anaemia is a common complication of diabetes mellitus (DM), usually related to renal failure. There is scarce information as to the levels of haemoglobin (Hb) and the rate of anaemia in diabetic patients with normal renal function. We, therefore, evaluated haemoglobin levels and the rate of anaemia in diabetic subjects with normal renal functions [estimated glomerular filtration rate (eGFR) > 60 mL/min].
Documenting Pornography Use in America: A Comparative Analysis of Methodological Approaches

Estimates of pornography use in the United States range widely. We explore the reasons for the variation in such estimates among U.S. adults using data from four different recent nationally representative samples—each of which asked a different type of question about pornography use. We attribute the notable variation in estimates to differences in question wording and answer options, and assert that a survey question asking respondents about their most recent use of pornography minimizes recall bias and is better poised to assess the overall prevalence of pornography in a population than is the more common approach of asking respondents about their historical general-use pattern. When we privileged the most-recent-use approach, survey data from 2014 reveal that 46% of men and 16% of women between the ages of 18 and 39 intentionally viewed pornography in a given week. These numbers are notably higher than most previous population estimates employing different types of questions. The results have ramifications for methods of surveying sensitive self-reported behaviors and for contextualizing scholars’ claims as well as popular conversations about the reach and implications of pornography use in the United States.
Preliminary results of multicenter questionnaire study on long‐term outcomes of curative endoscopic submucosal dissection for early gastric cancer

There are a number of published reports on long‐term outcomes of endoscopic submucosal dissection (ESD) for early gastric cancer (EGC), but most reports are from single centers with median follow‐up periods shorter than 5 years. This questionnaire study investigated long‐term outcomes of curative ESD for EGC at six Japanese institutions with follow‐up rates of at least 90% over a minimum 5‐year period.
Metformin and pathologic complete responses to neoadjuvant chemotherapy in diabetic patients with breast cancer.

PURPOSE Population studies have suggested that metformin use in diabetic patients decreases cancer incidence and mortality. Metformin inhibits the growth of cancer cells in vitro and tumors in vivo. However, there is little clinical data to support this. Our purpose was to determine whether metformin use was associated with a change in pathologic complete response (pCR) rates in diabetic patients with breast cancer receiving neoadjuvant chemotherapy. PATIENTS AND METHODS We identified 2,529 patients who received neoadjuvant chemotherapy for early-stage breast cancer between 1990 and 2007. Patients were compared by groups: 68 diabetic patients taking metformin, 87 diabetic patients not taking metformin, and 2,374 nondiabetic patients. pCR rates were compared between the three groups using chi(2) tests of independence and compared pair- wise using a binomial test of proportions. Factors predictive of pCR were assessed using a multivariate logistic regression model. RESULTS The rate of pCR was 24% in the metformin group, 8.0% in the nonmetformin group, and 16% in the nondiabetic group (P = .02). Pairwise comparisons between the metformin and nonmetformin groups (P = .007) and the nonmetformin and nondiabetic groups (P = .04) were significant. Comparison of the pCR rates between the metformin and nondiabetic groups trended toward but did not meet significance (P = .10). Metformin use was independently predictive of pCR (odds ratio, 2.95; P = .04) after adjustment for diabetes, body mass index, age, stage, grade, receptor status, and neoadjuvant taxane use. CONCLUSION Diabetic patients with breast cancer receiving metformin and neoadjuvant chemotherapy have a higher pCR rate than do diabetics not receiving metformin. Additional studies to evaluate the potential of metformin as an antitumor agent are warranted.
Globalizing the treadmill of production: a solutions-oriented application to Ecuador

ABSTRACT A foundational theory in environmental sociology, Allan Schnaiberg’s treadmill of production theory (1980), and subsequent elaborations of the treadmill of production theory, is best known and used to explain how societies have created environmental and social disruptions. Less well known and less utilized aspects of the original theory include proposed strategies to slow the treadmill of production, with the goals of decreasing withdrawals and additions, and increasing social justice. This paper revisits Schnaiberg’s original conceptualization of the treadmill of production theory to: (1) highlight and reinvigorate these under utilized portions of the theory, (2) apply the theory’s social change model to explain the case of Ecuador’s changing development trajectory from the 1970s to 2017, and (3) develop an aspect of the theory that was not in Schnaiberg’s original conceptualization; namely, how pressure from the global political economy affects states’ choices, and ultimately, their choices about social-environmental development trajectories. The broader goal of the paper is to contribute to public environmental sociologists’ quest to understand the conditions and the actions that offer the most promise for solving the intertwined social-environmental problems in a globalized political economy.
Corporate entity representatives of business group and real earnings management: evidence from Taiwan

ABSTRACT This study investigates how corporate entity directors and supervisors from business groups influence real earnings management (REM) by using a sample of firms listed on the Taiwan Stock Exchange. Our results show that firms with more corporate entity representatives are more likely to manipulate earnings upward through sales manipulation, overproduction, and reduction of discretionary expenditure. Prior studies focus on the effects of pyramid structures and cross-shareholdings. Our results contribute to provide new evidence that corporate entity representatives may increase agency costs and aggravate REM.
Environmental change and migration

West Africa is considered one of the world’s regions that is presumed to be highly affected by climate and environmental changes in the future (IPCC 2007). The majority of the rural population in the region depends on small-scale agriculture, crop production and livestock farming, and therefore on the natural environment. Environmental changes can thus constitute a severe threat to people’s livelihoods. Mobility in West Africa has a long tradition and the seasonality of rainfall influences the mobility patterns. Agricultural activities depend on only one rainy season in which the workload in agriculture is high. The seasonal movements of pastoralists with their animals to pasture grounds or the labour migration of farmers during the dry season are well-established patterns of migration (Davies 1996; Ellis 1998; Rain 1999). Main destinations are urban areas or more productive rural areas, either within the country or in neighbouring countries. The most established inter-regional mobility pattern in West Africa was and still is the North-South movement from the Sahelian landlocked countries of Burkina Faso, Mali and Niger to the coastal states, particularly to the economically strong Côte d’Ivoire. These patterns date back at least to the colonial area in the 19 century when plantation economies (e.g. cocoa, coffee, cotton, groundnut) attracted labour migrants from neighbouring countries and cities as Dakar, Abidjan, Lome and Accra benefited from investments for the export of goods to Europe (Hummel et al. 2012; Bakewell and de Haas 2007). Dryland West Africa has harsh environmental conditions and long established mobility patterns, but that does not necessarily mean that the two are related.
Hebb and Darwin.

It is proposed that vertebrate brains, especially those of mammals, operate according to an algorithm subsumable as "synaptic Darwinism". The key postulate is that genes and synapses follow the same rules, because they act as autocatalytic, hypercyclic, units of selection. Synapses replicate by quantally strengthening, and mutate by connecting new cells. Because synapses relate pre- and post-synaptic firing, they perform a translation operation. Furthermore the product of this operation, conjoint firing, favors replication (by Hebb's Rule). The result is that variants are selected and patterns of connection automatically adopt optimal configurations. These configurations are determined by scalar neuromodulatory "reward" signals applied globally to layers of neurons, which reduce spike frequency adaptation and enhance Hebbian replication. Global or local control of mutation rates provides further improvements in the Darwinian algorithm. All the processes and circuits postulated have plausible, and often obvious, implementations. The result is that brains evolve and adapt like large ecosystems.
Do Social Grants Displace Remittances? Evidence From South Africa

This paper employs a newly-available and representative National Income Dynamics Study (NIDS) data of South African households to investigate whether social grants crowd-out or displace remittances. The estimated results based on full sample reveal that while the social grants have a negative impact on the amount of remittances received, the effect is statistically insignificant – social grants do not crowd out or displace remittances. The coefficient on the social grant is also insignificant in both sub-samples (rural and urban), consistent with the results on the full sample
Inhibition of HIV‐1 replication by RNA interference of p53 expression

p53 expression and activation have been associated to faster human immunodeficiency virus (HIV) disease progression, most probably by inducing CD4+ T cell death but also through its cooperative effect in the control of viral gene transcription by viral regulatory proteins. Here, we show that RNA interference of p53 in HIV‐1 reporter (HeLa P4‐R5 MAGI) and lymphoid (SupT1) cell lines blocked HIV‐1 and Tat‐induced transcription from the HIV‐1 promoter and HIV‐1 replication in acutely infected cells, suggesting a cooperative role of p53 in HIV‐1 transcription. Contrary to SupT1 cells, which encoe several mutations on the p53 DNA binding domain, death of HIV‐1‐induced syncytia was reduced in cocultures of HeLa P4‐R5 MAGI with persistently infected HIV‐1 cells. To our knowledge, this is the first demonstration of the effect of the loss of function of p53 in HIV‐1 replication, which is independent on its classical DNA binding activity. Our results suggest two independent roles for p53 in HIV‐1 infection: cooperation in HIV long‐terminal repeat transcription and virus‐induced cell death.
Soluble suppression of tumorigenicity 2 (sST2), but not galactin‐3, adds to prognostication in patients with systemic AL amyloidosis independent of NT‐proBNP and troponin T

The use of soluble cardiac biomarkers such as N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) and troponin has revolutionized prognostication for patients with AL amyloidosis. Soluble ST2 (sST2) and galectin‐3 have also been reported to have prognostic value in other cardiac patient populations. We identified 502 patients with AL amyloidosis, who provided a research sample and consent to review their medical records between 1/1/2006‐12/31/2010 within 90 days of their diagnosis. Samples were assayed for sST2 and galectin‐3. Within this AL amyloidosis population, overall survival (OS) was 25.5 months (95% CI 18, 35.7 months). Receiver operating curve analyses were done to detect the best cut‐points for sST2 and galectin‐3 to predict both 1‐ and 5‐year OS. The respective cut points for sST2 were 30 and 29.7 ng/mL, while the median sST2 for the entire population was 31 ng/mL (IQR 19.8, 53.6). The respective cut points for galectin‐3 were 11 and 10.4 ng/mL while the median for the entire population was 16.6 ng/mL (IQR 11.5, 24.0). Although on univariate analysis, both sST2 and galectin‐3 were prognostic, upon multivariate analysis, only sST2 was independent of troponin, NT‐proBNP, serum immunoglobulin free light chain, and blood pressure. Not only did sST2 add to previously reported prognostication systems, but a novel prognostication 5‐point system including sST2 was possible. The addition of sST2 – but not galectin‐3 – to existing prognostication systems for patients with AL amyloidosis strengthens the ability to predict for death. Am. J. Hematol. 90:524–528, 2015. © 2015 Wiley Periodicals, Inc.
Long-term changes in the CA3 associative network of fear-conditioned mice

Abstract The CA3 associative network plays a critical role in the generation of network activity patterns related to emotional state and fear memory. We investigated long-term changes in the corticosterone (CORT)-sensitive function of this network following fear conditioning and fear memory reactivation. In acute slice preparations from mice trained in either condition, the ratio of orthodromic population spike (PS) to antidromic PS was reduced compared to unconditioned animals, indicating a decrease in efficacy of neuronal coupling within the associative CA3 network. However, spontaneous sharp wave–ripples (SW-R), which are thought to arise from this network, remained unaltered. Following CORT application, we observed an increase in orthodromic PS and a normalization to control levels of their ratio to antidromic PS, while SW-R increased in slices of fear conditioned and fear reactivated mice, but not in slices of unconditioned controls. Together with our previous observations of altered hippocampal gamma activity under these learning paradigms, these data suggest that fear conditioning and fear reactivation lastingly alters the CORT-sensitive configuration of different network activity patterns generated by the CA3 associational network. Observed changes in the mRNA expression of receptors for glutamate, GABA and cannabinoids in the stratum pyramidale of area CA3 may provide a molecular mechanism for these adaptive changes.
Examining the Development and Implementation of Functional Behavior Assessments and Behavior Intervention Plans through the Experiences of School Personnel

For school personnel, dedicating energy to addressing problem behaviors within the school setting becomes important when behaviors threaten the safety or disrupt the learning of the student and/or others (Anderson, Rodriquez, & Campbell, 2015). Not addressing problem behaviors may lead to a pattern of discipline referrals, which is likely to result in increased time out of the classroom (Anderson et al., 2015). Removal from the classroom further interrupts students’ ability to learn as they are missing valuable instruction while out of the classroom setting (Stephan, Connors, Arora, & Brey, 2013). At times school personnel are faced with working with students who exhibit problem behaviors. One approach recommended to help students manage behaviors in school is a functional behavior assessment (FBA) and the subsequent development of a behavior intervention plan (BIP). Using the lens of the Planning Realistic Implementation and Maintenance by Educators (PRIME) model (Sanetti et al., 2014), the purpose of the study was to gain an understanding of strategies used in the development and implementation of FBAs and BIPs from key stakeholders involved in the behavior management process in a school environment. The study highlights the training experiences of key school personnel in the behavior management process, giving support to the need for ongoing training opportunities for developing and implementing FBAs and BIPs. Results revealed that it is important to make sure everyone supporting the student is involved in the process. Results also highlight the important role school leaders hold in increasing the efficacy of student behavior plans. Document Type Dissertation Degree Name Doctor of Education (EdD) Department Executive Leadership First Supervisor Marie Cianca Subject Categories Education This dissertation is available at Fisher Digital Publications: https://fisherpub.sjfc. edu/education_etd/318 Examining the Development and Implementation of Functional Behavior Assessments and Behavior Intervention Plans through the Experiences of School Personnel By