Miracle-dz/UniFAR-FTUs huggingface dataset:
Seventeen Sxy-Dependent Cyclic AMP Receptor Protein Site-Regulated Genes Are Needed for Natural Transformation in Haemophilus influenzae

ABSTRACT Natural competence is the ability of bacteria to actively take up extracellular DNA. This DNA can recombine with the host chromosome, transforming the host cell and altering its genotype. In Haemophilus influenzae, natural competence is induced by energy starvation and the depletion of nucleotide pools. This induces a 26-gene competence regulon (Sxy-dependent cyclic AMP receptor protein [CRP-S] regulon) whose expression is controlled by two regulators, CRP and Sxy. The role of most of the CRP-S genes in DNA uptake and transformation is not known. We have therefore created in-frame deletions of each CRP-S gene and studied their competence phenotypes. All but one gene (ssb) could be deleted. Although none of the remaining CRP-S genes were required for growth in rich medium or survival under starvation conditions, DNA uptake and transformation were abolished or reduced in most of the mutants. Seventeen genes were absolutely required for transformation, with 14 of these genes being specifically required for the assembly and function of the type IV pilus DNA uptake machinery. Only five genes were dispensable for both competence and transformation. This is the first competence regulon for which all genes have been mutationally characterized.
Gender Differences in Medical Advice and Health Behavior of Obese African Americans With and Without Type 2 Diabetes

This study examined gender differences in medical advice related to diet and physical activity for obese African American adults (N = 470) with and without diabetes. Data from the 2007-2008 National Health and Nutrition Examination Survey were analyzed using logistic regression analyses. Even after sociodemographic adjustments, men were less likely to report receiving medical advice as compared with women. Both men and women given dietary and physical activity advice were more likely to follow it. Men were less likely to report currently reducing fat or calories, yet men with diabetes were 5 times more likely to state that they were reducing fat and calories as compared with women with diabetes. Gender- and disease state–specific interventions are needed comparing standard care with enhanced patient education. Moreover, these findings necessitate studies that characterize the role of the health care professional in the diagnosis and treatment of obesity and underscore patient–provider relationships.
A Bayesian Additive Model for Understanding Public Transport Usage in Special Events

Public special events, like sports games, concerts and festivals are well known to create disruptions in transportation systems, often catching the operators by surprise. Although these are usually planned well in advance, their impact is difficult to predict, even when organisers and transportation operators coordinate. The problem highly increases when several events happen concurrently. To solve these problems, costly processes, heavily reliant on manual search and personal experience, are usual practice in large cities like Singapore, London or Tokyo. This paper presents a Bayesian additive model with Gaussian process components that combines smart card records from public transport with context information about events that is continuously mined from the Web. We develop an efficient approximate inference algorithm using expectation propagation, which allows us to predict the total number of public transportation trips to the special event areas, thereby contributing to a more adaptive transportation system. Furthermore, for multiple concurrent event scenarios, the proposed algorithm is able to disaggregate gross trip counts into their most likely components related to specific events and routine behavior. Using real data from Singapore, we show that the presented model outperforms the best baseline model by up to 26 percent in R2 and also has explanatory power for its individual components.
CONGENITAL FAILURE OF AUTOMATIC CONTROL OF VENTILATION, GASTROINTESTINAL MOTILITY AND HEART RATE

: A new congenital syndrome characterized by the simultaneous failure of control of ventilation (Ondine's curse) and intestinal motility (Hirschsprung's disease) is reported in three infants, all of whom died in the first few months of life; two were siblings. Detailed studies in one also revealed markedly decreased esophageal motility and abnormal control of heart rate. In one infant, minute ventilation was lower in quiet than in REM sleep and lower in both states of sleep than in wakefulness. Although the mean inspiratory flow was decreased in quiet sleep, the hypoventilation resulted primarily from a decrease in respiratory frequency. Intravenous doxapram increased ventilation but did not reverse respiratory failure. Aminophyllin, progesterone, physostigmine and chlorpromazine did not change ventilation significantly; imipramine resulted in a significant decrease. Both long and short-term variability of the heart rate were markedly decreased when compared with the normal infant. Although neuropathologic studies postmorten did not reveal an anatomic defect, we postulate that a developmental abnormality in serotonergic neurons is responsible for this new syndrome.
Early Life Loss and Trauma

The onset of an eating disorder in middle-age men is poorly researched as are eating disorders in men generally. Therefore, life events that influence eating disorders in men, including delayed onset of an eating disorder remains unknown. Given the limited understanding of males with eating disorders and limited access to large samples of men with eating disorders, an in-depth analysis of a single case of a male in middle age with an eating disorder was chosen to gain insight and understanding into this phenomenon. A Life History approach explored the case of Joseph (pseudonym), who was diagnosed at age 44 years with an Eating Disorder Not Otherwise Specified. Data were collected through (a) life course open-ended questioning through interviews, (b) written statements, and (c) comments on transcripts. Three themes emerged, loss and unworthiness, becoming bigger, and wanting to change reflecting eating behaviors associated with attachment disruption, loss and trauma, body dissatisfaction, and negative affect. Later in life, an emotional “tipping point” precipitated an eating disorder. Results indicate traumatic loss leading to early attachment disruption as influential in Joseph’s delayed onset of an eating disorder. The value of thorough narrative life histories during therapy when eating disorders occur late in life is discussed as well as the significance for men.
Role of Ribonucleotide Reductase in Bacillus subtilis Stress-Associated Mutagenesis

ABSTRACT The Gram-positive microorganism Bacillus subtilis relies on a single class Ib ribonucleotide reductase (RNR) to generate 2′-deoxyribonucleotides (dNDPs) for DNA replication and repair. In this work, we investigated the influence of RNR levels on B. subtilis stationary-phase-associated mutagenesis (SPM). Since RNR is essential in this bacterium, we engineered a conditional mutant of strain B. subtilis YB955 (hisC952 metB5 leu427) in which expression of the nrdEF operon was modulated by isopropyl-β-d-thiogalactopyranoside (IPTG). Moreover, genetic inactivation of ytcG, predicted to encode a repressor (NrdR) of nrdEF in this strain, dramatically increased the expression levels of a transcriptional nrdE-lacZ fusion. The frequencies of mutations conferring amino acid prototrophy in three genes were measured in cultures under conditions that repressed or induced RNR-encoding genes. The results revealed that RNR was necessary for SPM and overexpression of nrdEF promoted growth-dependent mutagenesis and SPM. We also found that nrdEF expression was induced by H2O2 and such induction was dependent on the master regulator PerR. These observations strongly suggest that the metabolic conditions operating in starved B. subtilis cells increase the levels of RNR, which have a direct impact on SPM. IMPORTANCE Results presented in this study support the concept that the adverse metabolic conditions prevailing in nutritionally stressed bacteria activate an oxidative stress response that disturbs ribonucleotide reductase (RNR) levels. Such an alteration of RNR levels promotes mutagenic events that allow Bacillus subtilis to escape from growth-limited conditions.
Pneumococcal LytR, a Protein from the LytR-CpsA-Psr Family, Is Essential for Normal Septum Formation in Streptococcus pneumoniae

ABSTRACT Proliferation of the human-pathogenic bacterium Streptococcus pneumoniae is fundamentally linked to the bacterial proteins that function in cell division. Here, we show that LytR, a pneumococcal protein from the LytR-CpsA-Psr family, is essential to this process.
Conserved ABC Transport System Regulated by the General Stress Response Pathways of Alpha- and Gammaproteobacteria

ABSTRACT Brucella abortus σE1 is an EcfG family sigma factor that regulates the transcription of dozens of genes in response to diverse stress conditions and is required for maintenance of chronic infection in a mouse model. A putative ATP-binding cassette transporter operon, bab1_0223-bab1_0226, is among the most highly activated gene sets in the σE1 regulon. The proteins encoded by the operon resemble quaternary ammonium-compatible solute importers but are most similar in sequence to the broadly conserved YehZYXW system, which remains largely uncharacterized. Transcription of yehZYXW is activated by the general stress sigma factor σS in Enterobacteriaceae, which suggests a functional role for this transport system in bacterial stress response across the classes Alphaproteobacteria and Gammaproteobacteria. We present evidence that B. abortus YehZYXW does not function as an importer of known compatible solutes under physiological conditions and does not contribute to the virulence defect of a σE1-null strain. The sole in vitro phenotype associated with genetic disruption of this putative transport system is reduced growth in the presence of high Li+ ion concentrations. A crystal structure of B. abortus YehZ revealed a class II periplasmic binding protein fold with significant structural homology to Archaeoglobus fulgidus ProX, which binds glycine betaine. However, the structure of the YehZ ligand-binding pocket is incompatible with high-affinity binding to glycine betaine. This is consistent with weak measured binding of YehZ to glycine betaine and related compatible solutes. We conclude that YehZYXW is a conserved, stress-regulated transport system that is phylogenetically and functionally distinct from quaternary ammonium-compatible solute importers. IMPORTANCE Brucella abortus σE1 regulates transcription in response to stressors encountered in its mammalian host and is necessary for maintenance of chronic infection in a mouse model. The functions of the majority of genes regulated by σE1 remain undefined. We present a functional/structural analysis of a conserved putative membrane transport system (YehZYXW) whose expression is strongly activated by σE1. Though annotated as a quaternary ammonium osmolyte uptake system, experimental physiological studies and measured ligand-binding properties of the periplasmic binding protein (PBP), YehZ, are inconsistent with this function. A crystal structure of B. abortus YehZ provides molecular insight into differences between bona fide quaternary ammonium osmolyte importers and YehZ-related proteins, which form a distinct phylogenetic and functional group of PBPs.
An Overview of Testosterone Therapy

Millions of men, as a result of the natural aging process, injury, illness, and medical therapies, experience a decline in testosterone levels that necessitate a need for testosterone supplementation therapy (TST). The signs and symptoms of testosterone decline may occur gradually, and low testosterone levels may be misdiagnosed as other medical conditions. Over the past two decades, there has been an increase in testing of testosterone levels and the use of TST. With so many men now on TST, it is essential for health care professionals to know the signs and symptoms, the causes of testosterone decline, how testosterone deficiency is diagnosed, what pathological changes are associated with testosterone decline, and the benefits and risks of TST. In addition, health care providers need to be aware of the various forms of testosterone available as well as the advantages and disadvantages of each. This article provides a brief overview of testosterone deficiency, TST treatment options and guidelines, and the risks and benefits associated with of TST.
In Silico Identification and Experimental Characterization of Regulatory Elements Controlling the Expression of the Salmonella csrB and csrC Genes

ABSTRACT The small RNAs CsrB and CsrC of Salmonella indirectly control the expression of numerous genes encoding widespread cellular functions, including virulence. The expression of csrB and csrC genes, which are located in different chromosomal regions, is coordinated by positive transcriptional control mediated by the two-component regulatory system BarA/SirA. Here, we identified by computational analysis an 18-bp inverted repeat (IR) sequence located far upstream from the promoter of Salmonella enterica serovar Typhimurium csrB and csrC genes. Deletion analysis and site-directed mutagenesis of the csrB and csrC regulatory regions revealed that this IR sequence is required for transcriptional activation of both genes. Protein-DNA and protein-protein interaction assays showed that the response regulator SirA specifically binds to the IR sequence and provide evidence that SirA acts as a dimer. Interestingly, whereas the IR sequence was essential for the SirA-mediated expression of csrB, our results revealed that SirA controls the expression of csrC not only by binding to the IR sequence but also by an indirect mode involving the Csr system. Additional computational, biochemical, and genetic analyses demonstrated that the integration host factor (IHF) global regulator positively controls the expression of csrB, but not of csrC, by interacting with a sequence located between the promoter and the SirA-binding site. These findings contribute to the better understanding of the regulatory mechanism controlling the expression of CsrB and CsrC.
Dietary Patterns and Their Relationship With Semen Quality

Diet is a complex exposure variable, which calls for multiple approaches to examine the relationship between diet and disease risk. To address these issues, several authors have recently proposed studying overall dietary patterns by considering how foods and nutrients are consumed in combinations. The aim of the study was to investigate the associations between dietary patterns, semen quality parameters, and the level of reproductive hormones. The study population consisted of 336 men who attended the infertility clinic for diagnostic purposes and who had normal semen concentration of 20 to 300 mln/ml or slight oligozoospermia (semen concentration of 15-20 mln/ml). Participants were interviewed, and a semen sample was provided by them. Diet was assessed via food frequency questionnaire, and dietary patterns were identified by factor analysis. Men were classified into three groups according to scores of each dietary pattern: Western, Mixed, or Prudent. A positive association was observed between sperm concentration and Prudent dietary pattern, and level of testosterone and Prudent dietary pattern (p = .05, p = .03, respectively). Additionally, Prudent dietary pattern was identified to decrease the DNA fragmentation index (p = .05). The results were adjusted for sexual abstinence, age, smoking, past diseases, and alcohol consumption. Higher consumption of a Prudent dietary pattern was associated with higher sperm concentration and higher level of testosterone. Sperm chromatin structure was inversely related to higher consumption of a Prudent dietary pattern. Further research is needed to confirm these findings and extend these results to other populations.
A Study of Intimate Partner Violence, Substance Abuse, and Sexual Risk Behaviors Among Gay, Bisexual, and Other Men Who Have Sex With Men in a Sample of Geosocial-Networking Smartphone Application Users

Geosocial-networking smartphone applications (“apps”) are widely used by gay, bisexual, and other men who have sex with men (MSM) and facilitate connections between users based on proximity and attraction. MSM have sexual encounters and relationships of varying degrees of emotional and physical intimacy with app-met individuals, potentially placing them at risk for intimate partner violence (IPV). The purpose of the current study was to utilize a geosocial-networking application to investigate relationships between experiences of IPV victimization as it relates to substance use and sexual risk behaviors in a sample of MSM. Participants (n = 175) were recruited by means of broadcast advertisements on an application widely used by MSM (Grindr) to seek sexual partners. Multivariable regression models were fit to examine associations between IPV, substance abuse, and sexual risk behaviors. Lifetime experiences of IPV victimization were common, where 37.7% of respondents reported having experienced at least one form of IPV. While a marginally significant positive association between IPV and substance abuse was detected in multivariable models (p = .095), individual forms of IPV were strongly associated with substance abuse. For example, sexual IPV victimization was associated with an increase in substance abuse in the preceding month (p = .004). Experiences of IPV victimization were associated with higher numbers of partners for both condomless receptive and insertive anal intercourse (p < .05). Given the relatively high prevalence of IPV victimization and its associations with substance abuse and sexual risk behaviors, these findings suggest that IPV screening and prevention programs may reduce substance abuse and sexual risk behaviors in this population.
True ConvergeCast scheduling in Wireless Sensor Networks

An important application of Wireless Sensor Networks (WSNs) is target monitoring: sensors monitor a set of targets, and forward the collected data using multi-hop routing to the same location, called the sink. The resulting communication pattern is called ConvergeCast. Several researchers studied the problem of assigning TDMA time slots in order to minimize data collection time using mathematical programming models, with the claim that those models provide an optimal or a near-optimal ConvergeCast schedule. However, those models only output a multi-set of so-called transmission configurations, i.e., sets of links that can simultaneously transmit, and which together cover the links in all paths from sensors to the sink. In particular, these models do not provide an ordering of the transmission configurations, nor do they guarantee that such an ordering exists using no more than the minimum number of slots their model outputs. In this paper, we give for the first time, a mathematical programming formulation for a complete and optimal solution, i.e., an ordered sequence of transmission configurations that achieves ConvergeCast. This solution provides much better results than heuristic approaches in the literature, and a “true” scheduling in comparison with the previous mathematical programming approaches.
Effectiveness of Solifenacin for Managing of Bladder Spasms in Patients With Urethroplasty

To evaluate the efficacy and safety of solifenacin in the treatment of bladder spasms after urethroplasty. Patients underwent urethroplasty were randomly assigned to the study group (n = 165) and the control group (n = 150). Patients in the study group were treated with solifenacin for 7 days. Patients in the control group were placebo. Each group was further divided into four subgroups: paracentetic suprapubic cystostomy subgroup, traditional suprapubic cystostomy subgroup, former suprapubic cystostomy subgroup, and urethral catheter subgroup. A visual analogue scale (VAS) was used to measure the severity of bladder spasms. The mean duration of spasms, the frequency of spasms, and the incidences of urine extravasation and radiating pain were recorded each day. There were no significant differences in the VAS scores and mean duration of bladder spasms between the study and control groups . However, there was a significantly lower VAS score in the patients taking solifenacin in the paracentetic suprapubic cystostomy subgroup (p < .05). A similar tendency was noted in the mean duration of bladder spasms in this subgroup. In a comparison of the daily and nightly frequency of spasms within the four subgroups, a significant improvement was noted in the control group within 5 days. A similar difference was not noted within 6 days in the study group. The short-term therapy with solifenacin is an effective and safe method for decreasing the frequency of bladder spasms after urethroplasty. Patients undergoing paracentetic suprapubic cystostomy might be the only subset to benefit from this treatment.
Tumors of the Jugular Foramen: Diagnosis and Management

OBJECTIVE: Jugular foramen tumors are rare cranial base lesions that present diagnostic and management difficulties. With the availability of new diagnostic procedures these tumors have been more precisely studied and questions of whether, when, and how these lesions should be treated often arise. Data from 106 consecutive patients surgically treated in the past 17 years were retrospectively analyzed to identify surgical outcomes. METHODS: The tumors were approached by a multidisciplinary team composed of neurosurgeons, ear, nose, and throat surgeons, and neuroradiologists. Hypervascular lesions were embolized 3 to 5 days before surgery. The same surgical technique was used to resect all tumors. The surgical defect was covered with vascularized myofascial flaps. The internal carotid artery was infiltrated in two patients, and a saphenous graft bypass was carried out before removal of the lesions. The facial nerve was reconstructed with nerve grafts (great auricular nerve) or XII/VII anastomosis in five cases. Postoperative radiotherapy was carried out for malignant and invasive tumors. RESULTS: Paragangliomas were the most frequent lesions, followed by schwannomas and meningiomas. Complete excision was possible in 89% of benign tumors and 80% of paragangliomas. Lower cranial nerve deficit was the most frequent complication (10 patients, 9.4%), transient in 4 patients. Facial and cochlear nerve paralysis occurred in 8 patients (7.5%). The function of the facial nerve recovered spontaneously in 3 patients. Four patients (3.7%) developed postoperative cerebrospinal fluid leakage. Four patients (3.7%) died after surgery. CONCLUSION: Radical removal of benign jugular foramen tumors is the treatment of choice and may be curative. Large lesions can be radically excised in one surgical procedure with preservation of lower cranial nerves. Cranial base reconstruction with vascularized myofascial flaps reduces the incidence of postoperative cerebrospinal fluid leakage. Damage of the lower cranial nerves is the most serious surgical complication.