Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphoserine Phosphatase Is Required for Serine and One-Carbon Unit Synthesis in Hydrogenobacter thermophilus

ABSTRACT Hydrogenobacter thermophilus is an obligate chemolithoautotrophic bacterium of the phylum Aquificae and is capable of fixing carbon dioxide through the reductive tricarboxylic acid (TCA) cycle. The recent discovery of two novel-type phosphoserine phosphatases (PSPs) in H. thermophilus suggests the presence of a phosphorylated serine biosynthesis pathway; however, the physiological role of these novel-type metal-independent PSPs (iPSPs) in H. thermophilus has not been confirmed. In the present study, a mutant strain with a deletion of pspA, the catalytic subunit of iPSPs, was constructed and characterized. The generated mutant was a serine auxotroph, suggesting that the novel-type PSPs and phosphorylated serine synthesis pathway are essential for serine anabolism in H. thermophilus. As an autotrophic medium supplemented with glycine did not support the growth of the mutant, the reversible enzyme serine hydroxymethyltransferase does not appear to synthesize serine from glycine and may therefore generate glycine and 5,10-CH2-tetrahydrofolate (5,10-CH2-THF) from serine. This speculation is supported by the lack of glycine cleavage activity, which is needed to generate 5,10-CH2-THF, in H. thermophilus. Determining the mechanism of 5,10-CH2-THF synthesis is important for understanding the fundamental anabolic pathways of organisms, because 5,10-CH2-THF is a major one-carbon donor that is used for the synthesis of various essential compounds, including nucleic and amino acids. The findings from the present experiments using a pspA deletion mutant have confirmed the physiological role of iPSPs as serine producers and show that serine is a major donor of one-carbon units in H. thermophilus. IMPORTANCE Serine biosynthesis and catabolism pathways are intimately related to the metabolism of 5,10-CH2-THF, a one-carbon donor that is utilized for the biosynthesis of various essential compounds. For this reason, determining the mechanism of serine synthesis is important for understanding the fundamental anabolic pathways of microorganisms. In the present study, we experimentally confirmed that a novel phosphoserine phosphatase in the obligate chemolithoautotrophic bacterium Hydrogenobacter thermophilus is essential for serine biosynthesis. This finding indicates that serine is synthesized from an intermediate of gluconeogenesis in H. thermophilus. In addition, because glycine cleavage system activity and genes encoding an enzyme capable of producing 5,10-CH2-THF were not detected, serine appears to be the major one-carbon donor to tetrahydrofolate (THF) in H. thermophilus.
L₂ Kernel Classification

Nonparametric kernel methods are widely used and proven to be successful in many statistical learning problems. Well--known examples include the kernel density estimate (KDE) for density estimation and the support vector machine (SVM) for classification. We propose a kernel classifier that optimizes the L2 or integrated squared error (ISE) of a “difference of densities. ” We focus on the Gaussian kernel, although the method applies to other kernels suitable for density estimation. Like a support vector machine (SVM), the classifier is sparse and results from solving a quadratic program. We provide statistical performance guarantees for the proposed L2 kernel classifier in the form of a finite sample oracle inequality and strong consistency in the sense of both ISE and probability of error. A special case of our analysis applies to a previously introduced ISE-based method for kernel density estimation. For dimensionality greater than 15, the basic L2 kernel classifier performs poorly in practice. Thus, we extend the method through the introduction of a natural regularization parameter, which allows it to remain competitive with the SVM in high dimensions. Simulation results for both synthetic and real-world data are presented.
The Genain Quadruplets: A Case Study and Theoretical Analysis of Heredity and Environment in Schizophrenia

An unprecedented opportunity for the study of heredity and environment in mental illness was presented by monozygotic quadruplets, all schizophrenic. The National Institute of Mental Health, undertaking such a study, had these four girls live at the Institute for three years and subjected them and their parents to a variety of investigative procedures. Unfortunately, there seems to have been little advance planning. Rosenthal, the editor of the report and author of several chapters, apparently was not part of the original research team, but has made a valiant effort to coordinate the mass of accumulated data. Relatively little information is offered about possible inheritance, although the artificial name chosen, Genain , means "dreadful gene. " A geneticist explains why he considered the probability was over 99% that these quads were truly monozygotic. It is mentioned that the paternal grandmother may have had paranoid schizophrenia, but no other data concerning family history of mental
Electrical Stimulation of Eighth Cranial Nerve

This is a report concerning the methods by which we have succeeded in stimulating the eighth nerve electrically. To carry out this study certain postulates were made for the purpose of selecting the initial experiment. We first assumed that many patients suffering from congenital and acquired hearing loss harbored a defective or inadequate organ of Corti rather than a functionless auditory nerve. 1 It would follow therefore that we should attempt to develop a method of stimulating the never electrically, in a manner similar to that previously done by Djourno et al. 2 An additional postulate was that the individual nerve fibers of the auditory branch of the eighth nerve are nonspecific. We further assumed that the number of nerve fibers firing simultaneously is a function of the instantaneous sound intensity, that the number of serial firings per second is a function of frequency, and that interpretation of this
The C-Terminal Zwitterionic Sequence of CotB1 Is Essential for Biosilicification of the Bacillus cereus Spore Coat

ABSTRACT Silica is deposited in and around the spore coat layer of Bacillus cereus, and enhances the spore's acid resistance. Several peptides and proteins, including diatom silaffin and silacidin peptides, are involved in eukaryotic silica biomineralization (biosilicification). Homologous sequence search revealed a silacidin-like sequence in the C-terminal region of CotB1, a spore coat protein of B. cereus. The negatively charged silacidin-like sequence is followed by a positively charged arginine-rich sequence of 14 amino acids, which is remarkably similar to the silaffins. These sequences impart a zwitterionic character to the C terminus of CotB1. Interestingly, the cotB1 gene appears to form a bicistronic operon with its paralog, cotB2, the product of which, however, lacks the C-terminal zwitterionic sequence. A ΔcotB1B2 mutant strain grew as fast and formed spores at the same rate as wild-type bacteria but did not show biosilicification. Complementation analysis showed that CotB1, but neither CotB2 nor C-terminally truncated mutants of CotB1, could restore the biosilicification activity in the ΔcotB1B2 mutant, suggesting that the C-terminal zwitterionic sequence of CotB1 is essential for the process. We found that the kinetics of CotB1 expression, as well as its localization, correlated well with the time course of biosilicification and the location of the deposited silica. To our knowledge, this is the first report of a protein directly involved in prokaryotic biosilicification. IMPORTANCE Biosilicification is the process by which organisms incorporate soluble silicate in the form of insoluble silica. Although the mechanisms underlying eukaryotic biosilicification have been intensively investigated, prokaryotic biosilicification was not studied until recently. We previously demonstrated that biosilicification occurs in Bacillus cereus and its close relatives, and that silica is deposited in and around a spore coat layer as a protective coating against acid. The present study reveals that a B. cereus spore coat protein, CotB1, which carried a C-terminal zwitterionic sequence, is essential for biosilicification. Our results provide the first insight into mechanisms required for biosilicification in prokaryotes.
The Autolysin LytA Contributes to Efficient Bacteriophage Progeny Release in Streptococcus pneumoniae

ABSTRACT Most bacteriophages (phages) release their progeny through the action of holins that form lesions in the cytoplasmic membrane and lysins that degrade the bacterial peptidoglycan. Although the function of each protein is well established in phages infecting Streptococcus pneumoniae, the role—if any—of the powerful bacterial autolysin LytA in virion release is currently unknown. In this study, deletions of the bacterial and phage lysins were done in lysogenic S. pneumoniae strains, allowing the evaluation of the contribution of each lytic enzyme to phage release through the monitoring of bacterial-culture lysis and phage plaque assays. In addition, we assessed membrane integrity during phage-mediated lysis using flow cytometry to evaluate the regulatory role of holins over the lytic activities. Our data show that LytA is activated at the end of the lytic cycle and that its triggering results from holin-induced membrane permeabilization. In the absence of phage lysin, LytA is able to mediate bacterial lysis and phage release, although exclusive dependence on the autolysin results in reduced virion egress and altered kinetics that may impair phage fitness. Under normal conditions, activation of bacterial LytA, together with the phage lysin, leads to greater phage progeny release. Our findings demonstrate that S. pneumoniae phages use the ubiquitous host autolysin to accomplish an optimal phage exiting strategy.
Ultrasound-Guided Robotic Enucleation of Pancreatic Neuroendocrine Tumors

Background. Pancreatic neuroendocrine tumors (PanNETs) are relatively rare neoplasms with a low to mild malignant potential. They can be further divided into functioning and nonfunctioning, according to their secretive activity. Surgery is an optimal approach, but the classic open approach is challenging, with some patients having long hospitalization and potentially life-threatening complications. The robotic approach for PanNETs may represent an option to optimize their management. Methods. We retrospectively reviewed our prospectively maintained databases from 2 high-volume Italian centers for pancreatic surgery. Demographics, pathological characteristics, perioperative outcome, and medium-term follow-up of patients who underwent robotic pancreatic enucleations were collected. Results. Twelve patients with final diagnosis of PanNET were included. The mean age of the patients was 53.8 years (25-77). The median body mass index was 26 (24-29). Three lesions were functioning insulinomas, while the others were nonfunctioning tumors. No deaths occurred. Mild postoperative complications occurred, except for 1 grade B pancreatic fistula. The mean postoperative stay was 3.9 days (2-5). Conclusions. Our results confirm that robotic enucleation is a feasible and safe approach for the treatment of PanNETs, with short hospital stay and low incidence of morbidity.
Employment and Diabetes: a Survey of the Prevalence of Diabetic Workers known by Occupational Physicians, and the Restrictions Placed on Diabetic Workers in Employment

A postal survey of occupational physicians identified a prevalence of known diabetes among workers of 7.5 per 1000. The prevalence of insulin‐treated diabetes was 2.6 per 1000 and of other diabetes was 4.9 per 1000. The figure for insulin‐treated diabetes is lower than expected from population studies. The restrictions placed on diabetic workers in employment include shift‐work, heights, dangerous areas, driving, civil aviation, emergency teams, offshore oil work, and work overseas. Certain companies within the chemical, oil, steel, confectionery, and drinks industries had lower than expected numbers of diabetic workers and merit further detailed study.
Discrete Mereotopology for Spatial Reasoning in Automated Histological Image Analysis

Discrete mereotopology (DM) is a first-order spatial logic that fuses together mereology (the theory of parthood relations) and topology to model discrete space. We show how a set of quasitopological functions defined within DM can be mapped to specific operators defined in mathematical morphology (MM) and easily implemented in scientific image processing programs. These functions provide the means to model topological properties of individual regions and spatial relations between them such as contact, overlap, and the relation of part to whole. DM not only extends the expressive power of image processing applications where mathematical morphology is used, but by functioning as a logic it also supplies the formal basis with which to prove the correctness of implemented algorithms as well as providing the computational basis to mechanically reason about segmented digital images using automated reasoning programs. In particular, we show how DM can supply a model-based and algorithmic context to the otherwise blind pixel-based image processing routines still dominating conventional imaging approaches. A number of worked examples drawn from the histological domain are given, including segmentation of cells in culture, identifying basal cell layers from stratified epithelia sections, and cell sorting in blood smears.
Genome Sequence of the Halotolerant Bacterium Imtechella halotolerans K1T

ABSTRACT We report the 3.087-Mb genome sequence of Imtechella halotolerans K1T, isolated from an estuarine water sample collected from Kochi, Kerala, India. Strain K1 was recently reported as a novel genus of the family Flavobacteriaceae.
Small RNAs Repress Expression of Polysaccharide Utilization Loci of Gut Bacteroides Species

ABSTRACT Bacteroides species can metabolize numerous plant polysaccharides and host glycans present in the mammalian gut. The regulatory systems governing the induction of particular polysaccharide utilization loci when the cognate glycan is present are known, but how expression is repressed when a higher-priority glycan is present is largely unknown. In this issue of the Journal of Bacteriology, Cao et al. (J. Bacteriol. 198:2410–2418, 2016, http://dx.doi.org/10.1128/JB.00381-16) reveal a conserved mechanism in Bacteroides whereby antisense small RNAs (sRNA) repress expression of genes involved in utilization of host glycans.
Are Leadership and Management Essential for Good Research? An Interview Study of Genetic Researchers

Principal investigators are responsible for a myriad of leadership and management activities in their work. The practices they use to navigate these responsibilities ultimately influence the quality and integrity of research. However, leadership and management roles in research have received scant empirical examination. Semi-structured interviews with 32 National Institutes of Health (NIH)-funded genetic researchers revealed that they considered leadership and management essential for effective research, but their scientific training inadequately prepared them. We also report management practices that the researchers described using in their labs, as well as their perceptions of a proposed intervention to enhance laboratory leadership. These findings suggest best practices for the research community, future directions for scientific training, and implications for research on leadership and management in science.
An Assessment of a Shortened Consent Form for the Storage and Research Use of Residual Newborn Screening Blood Spots

As state newborn screening programs develop approaches to parental permission for the storage and use of residual dried newborn screening samples, it is important to understand how the public comprehends the consent elements. Focus groups in Utah, California, and Michigan (n = 7 groups, 69 participants) were conducted to evaluate the language on a shortened consent form. Outcomes from the analysis included barriers to conceptualizing biospecimen research, the overly cautious tone and awkwardness of the consent form, and perceptions of community versus individual benefit. This research offers insight on public response to, and comprehension of, commonly used consent language for the storage and use of dried blood spot research in a shortened consent form.
Regulation of nleA in Shiga Toxin-Producing Escherichia coli O84:H4 Strain 4795/97

ABSTRACT Many Shiga toxin-producing Escherichia coli (STEC) strains express a type III secretion system (TTSS) encoded by the locus of enterocyte effacement (LEE). Using the TTSS, STEC is able to inject effector proteins directly into eukaryotic host cells, where they cause characteristic attaching and effacing (A/E) lesions. In addition to the LEE-encoded effectors, a number of non-LEE-encoded effectors, located on phage-associated elements, have been described. One of them, the non-LEE-encoded effector A (NleA), is widely distributed among pathogenic E. coli. In this study, we investigated the influence of environmental conditions on the expression of the phage-encoded effector nleA gene (designated nleA4795) present in STEC O84:H4 strain 4795/97. We demonstrated that a particular NaCl concentration and starvation stress increase the activity of the nleA4795 promoter. Moreover, several regulators that control nleA4795 expression were identified. The involvement of the LEE regulators Ler, GrlA, and GrlR show that nleA4795 is integrated in the LEE regulation circuit. Furthermore, the binding of Ler to sequences upstream of nleA4795 underlined these findings.
Racial/Ethnic Disparities and Culturally Competent Health Care Among Youth and Young Men

Racial/ethnic disparities in health and health care are receiving increasing national attention from the fields of public health and medicine. Efforts to reduce disparities should adopt a life-span approach and recognize the role of gender. During adolescence, young people make increasingly independent decisions about health-related behavior and health care, while developing gender identity. Little is known about how cultural context shapes gender identity and gender identity's influence on health-related behavior and health care utilization. The authors review disparities in health status and health care among adolescents, especially young men, by reviewing health care access, clinical services, and issues related to culture, identity, and acculturation. Significant differences in health status by gender exist in adolescence, with young men faring worse on many health markers. This article discusses gaps in research and offers recommendations for improving health care quality and strengthening the research base on gender and disparities during adolescence.
NADP+ Reduction with Reduced Ferredoxin and NADP+ Reduction with NADH Are Coupled via an Electron-Bifurcating Enzyme Complex in Clostridium kluyveri

ABSTRACT It was recently found that the cytoplasmic butyryl-coenzyme A (butyryl-CoA) dehydrogenase-EtfAB complex from Clostridium kluyveri couples the exergonic reduction of crotonyl-CoA to butyryl-CoA with NADH and the endergonic reduction of ferredoxin with NADH via flavin-based electron bifurcation. We report here on a second cytoplasmic enzyme complex in C. kluyveri capable of energetic coupling via this novel mechanism. It was found that the purified iron-sulfur flavoprotein complex NfnAB couples the exergonic reduction of NADP+ with reduced ferredoxin (Fdred) and the endergonic reduction of NADP+ with NADH in a reversible reaction: Fdred2− + NADH + 2 NADP+ + H+ = Fdox + NAD+ + 2 NADPH. The role of this energy-converting enzyme complex in the ethanol-acetate fermentation of C. kluyveri is discussed.
Genome Sequence of a Novel Human Pathogen, Aeromonas aquariorum

ABSTRACT Aeromonas aquariorum, a recently described species, is associated with a variety of human diseases. We present here the first genome sequence of A. aquariorum strain AAk1, which was isolated as the sole pathogen from the blood of a patient with septicemia and necrotizing fasciitis.
Joint A Contrario Ellipse and Line Detection

We propose a line segment and elliptical arc detector that produces a reduced number of false detections on various types of images without any parameter tuning. For a given region of pixels in a grey-scale image, the detector decides whether a line segment or an elliptical arc is present (model validation). If both interpretations are possible for the same region, the detector chooses the one that best explains the data (model selection ). We describe a statistical criterion based on the a contrario theory, which serves for both validation and model selection. The experimental results highlight the performance of the proposed approach compared to state-of-the-art detectors, when applied on synthetic and real images.
Transcriptional Repression Mediated by a TetR Family Protein, PfmR, from Thermus thermophilus HB8

ABSTRACT PfmR is one of four TetR family transcriptional regulators found in the extremely thermophilic bacterium, Thermus thermophilus HB8. We identified three promoters with strong negative regulation by PfmR, both in vivo and in vitro. PfmR binds pseudopalindromic sequences, with the consensus sequence of 5′-TACCGACCGNTNGGTN-3′ surrounding the promoters. According to the amino acid sequence and three-dimensional structure analyses of the PfmR-regulated gene products, they are predicted to be involved in phenylacetic acid and fatty acid metabolism. In vitro analyses revealed that PfmR weakly cross-regulated with the TetR family repressor T. thermophilus PaaR, which controls the expression of the paa gene cluster putatively involved in phenylacetic acid degradation but not with another functionally identified TetR family repressor, T. thermophilus FadR, which is involved in fatty acid degradation. The X-ray crystal structure of the N-terminal DNA-binding domain of PfmR and the nucleotide sequence of the predicted PfmR-binding site are quite similar to those of the TetR family repressor QacR from Staphylococcus aureus. Similar to QacR, two PfmR dimers bound per target DNA. The bases recognized by QacR within the QacR-binding site are conserved in the predicted PfmR-binding site, and they were important for PfmR to recognize the binding site and properly assemble on it. The center of the PfmR molecule contains a tunnel-like pocket, which may be the ligand-binding site of this regulator.
Are Men More Intuitive When It Comes to Eating and Physical Activity?

The purpose of this study was to determine where men fall on the motivation continuum based on intuitive eating status and if motivation for physical activity and intuitive eating are correlated. Results indicate that being an intuitive eater was associated with a lower body mass index. In terms of demographic variables, as age increased, intuitive eating status decreased and body mass index increased. Men scored high on the antidieting and self-care subscales of the Intuitive Eating Scale. Men who were classified as intuitive eaters scored higher on the external and introjected regulation of the Behavioral Regulation in Exercise Questionnaire but no significant differences were reported by eating status and the identified and intrinsic motivation subscales. Intuitive eating holds promise as a weight management and weight loss tool for men. Intuitive eating may also influence initial motivation for physical activity for men.