Miracle-dz/UniFAR-FTUs huggingface dataset:
Cupriavidus necator H16 Uses Flavocytochrome c Sulfide Dehydrogenase To Oxidize Self-Produced and Added Sulfide

ABSTRACT Production of sulfide (H2S, HS−, and S2−) by heterotrophic bacteria during aerobic growth is a common phenomenon. Some bacteria with sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO) can oxidize self-produced sulfide to sulfite and thiosulfate, but other bacteria without these enzymes release sulfide into the medium, from which H2S can volatilize into the gas phase. Here, we report that Cupriavidus necator H16, with the fccA and fccB genes encoding flavocytochrome c sulfide dehydrogenases (FCSDs), also oxidized self-produced H2S. A mutant in which fccA and fccB were deleted accumulated and released H2S. When fccA and fccB were expressed in Pseudomonas aeruginosa strain Pa3K with deletions of its sqr and pdo genes, the recombinant rapidly oxidized sulfide to sulfane sulfur. When PDO was also cloned into the recombinant, the recombinant with both FCSD and PDO oxidized sulfide to sulfite and thiosulfate. Thus, the proposed pathway is similar to the pathway catalyzed by SQR and PDO, in which FCSD oxidizes sulfide to polysulfide, polysulfide spontaneously reacts with reduced glutathione (GSH) to produce glutathione persulfide (GSSH), and PDO oxidizes GSSH to sulfite, which chemically reacts with polysulfide to produce thiosulfate. About 20.6% of sequenced bacterial genomes contain SQR, and only 3.9% contain FCSD. This is not a surprise, since SQR is more efficient in conserving energy because it passes electrons from sulfide oxidation into the electron transport chain at the quinone level, while FCSD passes electrons to cytochrome c. The transport of electrons from the latter to O2 conserves less energy. FCSDs are grouped into three subgroups, well conserved at the taxonomic level. Thus, our data show the diversity in sulfide oxidation by heterotrophic bacteria. IMPORTANCE Heterotrophic bacteria with SQR and PDO can oxidize self-produced sulfide and do not release H2S into the gas phase. C. necator H16 has FCSD but not SQR, and it does not release H2S. We confirmed that the bacterium used FCSD for the oxidation of self-produced sulfide. The bacterium also oxidized added sulfide. The common presence of SQRs, FCSDs, and PDOs in heterotrophic bacteria suggests the significant role of heterotrophic bacteria in sulfide oxidation, participating in sulfur biogeochemical cycling. Further, FCSDs have been identified in anaerobic photosynthetic bacteria and chemolithotrophic bacteria, but their physiological roles are unknown. We showed that heterotrophic bacteria use FCSDs to oxidize self-produced sulfide and extraneous sulfide, and they may be used for H2S bioremediation.
Prediction of psychological outcomes one year after a motor vehicle accident.

OBJECTIVE The authors' goal was to identify predictors of 1-year outcomes for consecutive patients in a hospital emergency department following motor vehicle accidents and to describe the prevalence and course of four types of psychiatric outcomes after such accidents. METHOD Consecutive patients aged 17-69 years who attended a general hospital emergency department following a motor vehicle accident were identified. Medical information for these patients was extracted from case notes, and the patients completed self-report questionnaires at baseline (soon after the accident), 3 months after the accident, and 1 year after the accident. Measures included a self-report scale for posttraumatic stress disorder (PTSD), the Hospital Anxiety and Depression Scale, and questions about phobic travel anxiety. Logistic regression was used to examine predictors of outcome. RESULTS Different frequencies and courses of PTSD, phobic travel anxiety, general anxiety, and depression were reported by a third of the subjects at both 3-month and 1-year follow-up. Many of the subjects reported improvements between 3 and 12 months, but others described late onset of psychiatric outcomes after the accident. There were differences in baseline and 3-month predictors of each type of 1-year outcome. CONCLUSIONS The four types of psychiatric outcomes after a motor vehicle accident that were noted overlap, are persistent, and have different early predictors. These findings have implications for the early recognition of psychiatric consequences of motor vehicle accidents that would enable early intervention.
Frequency and Dendritic Distribution of Autapses Established by Layer 5 Pyramidal Neurons in the Developing Rat Neocortex: Comparison with Synaptic Innervation of Adjacent Neurons of the Same Class

Synaptic contacts formed by the axon of a neuron on its own dendrites are known as autapses. Autaptic contacts occur frequently in cultured neurons and have been considered to be aberrant structures. We examined the regular occurrence, dendritic distribution, and fine structure of autapses established on layer 5 pyramidal neurons in the developing rat neocortex. Whole-cell recordings were made from single neurons and synaptically coupled pairs of pyramidal cells, which were filled with biocytin, morphologically reconstructed, and quantitatively analyzed. Autapses were found in most neurons (in 80% of all cells analyzed; n = 41). On average, 2.3 ± 0.9 autapses per neuron were found, located primarily on basal dendrites (64%; 50–70 μm from the soma), to a lesser extent on apical oblique dendrites (31%; 130–200 μm from the soma), and rarely on the main apical dendrite (5%; 480–540 μm from the soma). About three times more synaptic than autaptic contacts (ratio 2.4:1) were formed by a single adjacent synaptically coupled neuron of the same type. The dendritic locations of these synapses were remarkably similar to those of autapses. Electron microscopic examination of serial ultrathin sections confirmed the formation of autapses and synapses, respectively, and showed that both types of contacts were located either on dendritic spines or shafts. The similarities between autapses and synapses suggest that autaptic and synaptic circuits are governed by some common principles of synapse formation.
A Clinical Predictor Score for 30-Day Mortality among HIV-Infected Adults Hospitalized with Pneumonia in Uganda

Background Pneumonia is a major cause of mortality among HIV-infected patients. Pneumonia severity scores are promising tools to assist clinicians in predicting patients’ 30-day mortality, but existing scores were developed in populations infected with neither HIV nor tuberculosis (TB) and include laboratory data that may not be available in resource-limited settings. The objective of this study was to develop a score to predict mortality in HIV-infected adults with pneumonia in TB-endemic, resource-limited settings. Methods We conducted a secondary analysis of data from a prospective study enrolling HIV-infected adults with cough ≥2 weeks and <6 months and clinically suspected pneumonia admitted to Mulago Hospital in Kampala, Uganda from September 2008 to March 2011. Patients provided two sputum specimens for mycobacteria, and those with Ziehl-Neelsen sputum smears that were negative for mycobacteria underwent bronchoscopy with inspection for Kaposi sarcoma and testing for mycobacteria and fungi, including Pneumocystis jirovecii. A multivariable best subsets regression model was developed, and one point was assigned to each variable in the model to develop a clinical predictor score for 30-day mortality. Results Overall, 835 patients were studied (mean age 34 years, 53.4% female, 30-day mortality 18.2%). A four-point clinical predictor score was identified and included heart rate >120 beats/minute, respiratory rate >30 breaths/minute, oxygen saturation <90%, and CD4 cell count <50 cells/mm3. Patients’ 30-day mortality, stratified by score, was: score 0 or 1, 12.6%, score 2 or 3, 23.4%, score 4, 53.9%. For each 1 point change in clinical predictor score, the odds of 30-day mortality increased by 65% (OR 1.65, 95% CI 1.39-1.96, p <0.001). Conclusions A simple, four-point scoring system can stratify patients by levels of risk for mortality. Rapid identification of higher risk patients combined with provision of timely and appropriate treatment may improve clinical outcomes. This predictor score should be validated in other resource-limited settings.
Computable Jordan Decomposition of Linear Continuous Functionals on $C[0;1]$

By the Riesz representation theorem using the Riemann-Stieltjes integral, linear continuous functionals on the set of continuous functions from the unit interval into the reals can either be characterized by functions of bounded variation from the unit interval into the reals, or by signed measures on the Borel-subsets. Each of these objects has an (even minimal) Jordan decomposition into non-negative or non-decreasing objects. Using the representation approach to computable analysis, a computable version of the Riesz representation theorem has been proved by Jafarikhah, Lu and Weihrauch. In this article we extend this result. We study the computable relation between three Banach spaces, the space of linear continuous functionals with operator norm, the space of (normalized) functions of bounded variation with total variation norm, and the space of bounded signed Borel measures with variation norm. We introduce natural representations for defining computability. We prove that the canonical linear bijections between these spaces and their inverses are computable. We also prove that Jordan decomposition is computable on each of these spaces.
Diabetogenic Potential of Ancestral and Modern Wheat Landraces

Dear Editor, We read with interest the article by Gorelick et al. [1], who assayed the diabetogenic potential of two ancestral wheat landraces (Triticum turgidum ssp. dicoccoides and spp. dicoccum), compared to a modern wheat cultivar (T. aestivum) in NOD mice. [. ].
Pediatric Differentiated Thyroid Carcinoma in The Netherlands: A Nationwide Follow-Up Study.

INTRODUCTION Treatment for differentiated thyroid carcinoma (DTC) in pediatric patients is based mainly on evidence from adult series due to lack of data from pediatric cohorts. Our objective was to evaluate presentation, treatment-related complications, and long-term outcome in patients with pediatric DTC in The Netherlands. PATIENTS AND METHODS In this nationwide study, presentation, complications, and outcome of patients with pediatric DTC (age at diagnosis ≤18 y) treated in The Netherlands between 1970 and 2013 were assessed using medical records. RESULTS We identified 170 patients. Overall survival was 99.4% after a median follow-up of 13.5 years (range 0.3-44.7 y). Extensive follow-up data were available for 105 patients (83.8% women), treated in 39 hospitals. Median age at diagnosis was 15.6 years (range 5.8-18.9 y). At initial diagnosis, 43.8% of the patients had cervical lymph node metastases; 13.3% had distant metastases. All patients underwent total thyroidectomy. Radioiodine was administered to 97.1%, with a median cumulative activity of 5.66 GBq (range 0.74-35.15 GBq). Life-long postoperative complications (permanent hypoparathyroidism and/or recurrent laryngeal nerve injury) were present in 32.4% of the patients. At last known follow-up, 8.6% of the patients had persistent disease and 7.6% experienced a recurrence. TSH suppression was not associated with recurrences (odds ratio 2.00, 95% confidence interval 0.78-5.17, P = .152). CONCLUSIONS Survival of pediatric DTC is excellent. Therefore, minimizing treatment-related morbidity takes major priority. Our study shows a frequent occurrence of life-long postoperative complications. Adverse effects may be reduced by the centralization of care, which is crucial for children with DTC.
MTERF3 Regulates Mitochondrial Ribosome Biogenesis in Invertebrates and Mammals

Regulation of mitochondrial DNA (mtDNA) expression is critical for the control of oxidative phosphorylation in response to physiological demand, and this regulation is often impaired in disease and aging. We have previously shown that mitochondrial transcription termination factor 3 (MTERF3) is a key regulator that represses mtDNA transcription in the mouse, but its molecular mode of action has remained elusive. Based on the hypothesis that key regulatory mechanisms for mtDNA expression are conserved in metazoans, we analyzed Mterf3 knockout and knockdown flies. We demonstrate here that decreased expression of MTERF3 not only leads to activation of mtDNA transcription, but also impairs assembly of the large mitochondrial ribosomal subunit. This novel function of MTERF3 in mitochondrial ribosomal biogenesis is conserved in the mouse, thus we identify a novel and unexpected role for MTERF3 in coordinating the crosstalk between transcription and translation for the regulation of mammalian mtDNA gene expression.
Cooperation Network Structure and Individual Effectiveness in Knowledge-Intensive Organizations

This paper argues that an individual’s ability to add value in knowledge-intensive organizations depends on the structure of the networks in which the individual (ego) enacts her roles in the value creation process within the firm. The effects of network structure, however, vary across the two roles ego enact in that process: a producer role that links her to alters who provide inputs for her work, and a supplier role in which she interfaces with alters who demand her inputs for their work. A key differentiating element between the two roles is the need for alters’ cooperation. While cooperation can enhance ego’s effectiveness in the producer role, it is inconsequential in the supplier role. Consistent with this analysis, we show that the benefits of cooperation can initially offset the costs of information redundancy in the producer role, causing an inverted u-shaped relationship with the density of contacts among alters in that role. Effectiveness in the supplier role, however, is mostly affected by redundancy costs and thus it decreases linearly with the network density. Evidence comes from studying the effects of network structure on role effectiveness among a large sample of top employees working for the Equities division of a global securities firm.
Training a Natural Language Generator From Unaligned Data

We present a novel syntax-based natural language generation system that is trainable from unaligned pairs of input meaning representations and output sentences. It is divided into sentence planning, which incrementally builds deep-syntactic dependency trees, and surface realization. Sentence planner is based on A* search with a perceptron ranker that uses novel differing subtree updates and a simple future promise estimation; surface realization uses a rule-based pipeline from the Treex NLP toolkit. Our first results show that training from unaligned data is feasible, the outputs of our generator are mostly fluent and relevant.
The Procyclical Effects of Bank Capital Regulation

We assess the procyclical effects of bank capital regulation in a dynamic equilibrium model of relationship lending in which banks are unable to access the equity markets every period. Banks anticipate that shocks to their earnings as well as the cyclical position of the economy can impair their capacity to lend in the future and, as a precaution, hold capital buffers. We find that under cyclically-varying risk-based capital requirements (e.g. Basel II) banks hold larger buffers in expansions than in recessions. Yet, these buffers are insufficient to prevent a significant contraction in the supply of credit at the arrival of a recession. We show that cyclical adjustments in the confidence level underlying Basel II can reduce its procyclical effects on the supply of credit without compromising banks’ long-run solvency targets.
Real-time Dense Disparity Estimation based on Multi-Path Viterbi for Intelligent Vehicle Applications

This paper proposes a new real-time stereo matching algorithm paired with an online auto-rectification framework. The algorithm treats disparities of stereo images as hidden states and conducts Viterbi process at 4 bi-directional paths to estimate them. Structural similarity, total variation constraint, and a specific hierarchical merging strategy are combined with the Viterbi process to improve the robustness and accuracy. Based on the results of Viterbi, a convex optimization equation is derived to estimate epipolar line distortion. The estimated distortion information is used for the online compensation of Viterbi process at an auto-rectification framework. Extensive experiments were conducted to compare proposed algorithm with other practical state-of-the-art methods for intelligent vehicle applications.
Sentence Compression for Target-Polarity Word Collocation Extraction

Target-polarity word (T-P) collocation extraction, a basic sentiment analysis task, relies primarily on syntactic features to identify the relationships between targets and polarity words. A major problem of current research is that this task focuses on customer reviews, which are natural or spontaneous, thus posing a challenge to syntactic parsers. We address this problem by proposing a framework of adding a sentiment sentence compression (Sent Comp) step before performing T-P collocation extraction. Sent Comp seeks to remove the unnecessary information for sentiment analysis, thereby compressing a complicated sentence into one that is shorter and easier to parse. We apply a discriminative conditional random field model, with some special sentimentrelated features, in order to automatically compress sentiment sentences. Experiments show that Sent Comp significantly improves the performance of T-P collocation extraction.
Banner positioning in the masthead area of online newspapers: an eye tracking study

In this article we present an eye tracking investigation aimed at inspecting the eye behaviour of users while looking at the home page of online newspapers containing ad banners, especially during the first seconds of exposure. In particular, we consider different positions and combinations for banners placed in the masthead region of the page, to verify whether there are solutions that are better than others in catching the early attention of the user. The study involved 50 testers and was carried out on simulated newspaper home pages using a remote eye tracker. Although differences in testers' behaviours were not always statistically significant, some interesting divergences could however be identified, which can be the starting point for more focused studies on the subject.
Over-expression of Plk4 induces centrosome amplification, loss of primary cilia and associated tissue hyperplasia in the mouse

To address the long-known relationship between supernumerary centrosomes and cancer, we have generated a transgenic mouse that permits inducible expression of the master regulator of centriole duplication, Polo-like-kinase-4 (Plk4). Over-expression of Plk4 from this transgene advances the onset of tumour formation that occurs in the absence of the tumour suppressor p53. Plk4 over-expression also leads to hyperproliferation of cells in the pancreas and skin that is enhanced in a p53 null background. Pancreatic islets become enlarged following Plk4 over-expression as a result of equal expansion of α- and β-cells, which exhibit centrosome amplification. Mice overexpressing Plk4 develop grey hair due to a loss of differentiated melanocytes and bald patches of skin associated with a thickening of the epidermis. This reflects an increase in proliferating cells expressing keratin 5 in the basal epidermal layer and the expansion of these cells into suprabasal layers. Such cells also express keratin 6, a marker for hyperplasia. This is paralleled by a decreased expression of later differentiation markers, involucrin, filaggrin and loricrin. Proliferating cells showed an increase in centrosome number and a loss of primary cilia, events that were mirrored in primary cultures of keratinocytes established from these animals. We discuss how repeated duplication of centrioles appears to prevent the formation of basal bodies leading to loss of primary cilia, disruption of signalling and thereby aberrant differentiation of cells within the epidermis. The absence of p53 permits cells with increased centrosomes to continue dividing, thus setting up a neoplastic state of error prone mitoses, a prerequisite for cancer development.
Extensions and limits to vertex sparsification

Suppose we are given a graph G = (V, E) and a set of terminals K ⊂ V. We consider the problem of constructing a graph H = (K, EH) that approximately preserves the congestion of every multicommodity flow with endpoints supported in K. We refer to such a graph as a flow sparsifier. We prove that there exist flow sparsifiers that simultaneously preserve the congestion of all multicommodity flows within an O(log k / log log k)-factor where |K| = k. This bound improves to O(1) if G excludes any fixed minor. This is a strengthening of previous results, which consider the problem of finding a graph H = (K, EH) (a cut sparsifier) that approximately preserves the value of minimum cuts separating any partition of the terminals. Indirectly our result also allows us to give a construction for better quality cut sparsifiers (and flow sparsifiers). Thereby, we immediately improve all approximation ratios derived using vertex sparsification in [14]. We also prove an Ω(log log k) lower bound for how well a flow sparsifier can simultaneously approximate the congestion of every multicommodity flow in the original graph. The proof of this theorem relies on a technique (which we refer to as oblivious dual certifcates) for proving super-constant congestion lower bounds against many multicommodity flows at once. Our result implies that approximation algorithms for multicommodity flow-type problems designed by a black box reduction to a "uniform" case on k nodes (see [14] for examples) must incur a super-constant cost in the approximation ratio.
Use of Plasma Renin Activity to Monitor Mineralocorticoid Treatment in Dogs with Primary Hypoadrenocorticism: Desoxycorticosterone Versus Fludrocortisone

Background Measurement of plasma renin activity (PRA) is the gold standard for monitoring mineralocorticoid treatment in humans with primary hypoadrenocorticism (PH). Objectives To compare PRA in dogs with newly diagnosed PH, dogs with diseases mimicking PH, and healthy dogs, and evaluate measurement of PRA to monitor therapeutic effects in dogs with PH treated with different mineralocorticoids. Animals Eleven dogs with newly diagnosed PH (group 1), 10 dogs with diseases mimicking PH (group 2), 21 healthy dogs (group 3), 17 dogs with treated PH (group 4). Methods In group 1, PRA was measured before treatment and at different times after initiating treatment. In groups 2 and 3, PRA was measured at initial presentation only. In group 4, no baseline PRA was obtained but PRA was measured once or every 1–6 months during treatment. Mineralocorticoid treatment consisted of fludrocortisone acetate (FC) or desoxycorticosterone pivalate (DOCP). Results Plasma renin activity before treatment was increased in dogs with PH compared to normal dogs and dogs with diseases mimicking PH with median activity of 27, 0.8, and 1.0 ng/mL/h, respectively. In dogs with PH, PRA decreased and normalized with mineralocorticoid treatment using DOCP but not with FC. In dogs treated with DOCP, PRA was lower than in dogs treated with FC. Plasma sodium concentrations were higher and potassium concentrations were lower with DOCP treatment compared to FC treatment. Conclusion and Clinical Importance Plasma renin activity is a reliable tool for monitoring mineralocorticoid treatment. DOCP treatment more effectively suppresses PRA compared to FC in dogs with PH.