Miracle-dz/UniFAR-FTUs huggingface dataset:
Potential Effects of Horizontal Gene Exchange in the Human Gut

Many essential functions of the human body are dependent on the symbiotic microbiota, which is present at especially high numbers and diversity in the gut. This intricate host–microbe relationship is a result of the long-term coevolution between the two. While the inheritance of mutational changes in the host evolution is almost exclusively vertical, the main mechanism of bacterial evolution is horizontal gene exchange. The gut conditions, with stable temperature, continuous food supply, constant physicochemical conditions, extremely high concentration of microbial cells and phages, and plenty of opportunities for conjugation on the surfaces of food particles and host tissues, represent one of the most favorable ecological niches for horizontal gene exchange. Thus, the gut microbial system genetically is very dynamic and capable of rapid response, at the genetic level, to selection, for example, by antibiotics. There are many other factors to which the microbiota may dynamically respond including lifestyle, therapy, diet, refined food, food additives, consumption of pre- and probiotics, and many others. The impact of the changing selective pressures on gut microbiota, however, is poorly understood. Presumably, the gut microbiome responds to these changes by genetic restructuring of gut populations, driven mainly via horizontal gene exchange. Thus, our main goal is to reveal the role played by horizontal gene exchange in the changing landscape of the gastrointestinal microbiome and potential effect of these changes on human health in general and autoimmune diseases in particular.
Voluntary Exercise Prevents Cisplatin-Induced Muscle Wasting during Chemotherapy in Mice

Loss of muscle mass related to anti-cancer therapy is a major concern in cancer patients, being associated with important clinical endpoints including survival, treatment toxicity and patient-related outcomes. We investigated effects of voluntary exercise during cisplatin treatment on body weight, food intake as well as muscle mass, strength and signalling. Mice were treated weekly with 4 mg/kg cisplatin or saline for 6 weeks, and randomized to voluntary wheel running or not. Cisplatin treatment induced loss of body weight (29.8%, P < 0.001), lean body mass (20.6%, P = 0.001), as well as anorexia, impaired muscle strength (22.5% decrease, P < 0.001) and decreased glucose tolerance. In addition, cisplatin impaired Akt-signalling, induced genes related to protein degradation and inflammation, and reduced muscle glycogen content. Voluntary wheel running during treatment attenuated body weight loss by 50% (P < 0.001), maintained lean body mass (P < 0.001) and muscle strength (P < 0.001), reversed anorexia and impairments in Akt and protein degradation signalling. Cisplatin-induced muscular inflammation was not prevented by voluntary wheel running, nor was glucose tolerance improved. Exercise training may preserve muscle mass in cancer patients receiving cisplatin treatment, potentially improving physical capacity, quality of life and overall survival.
Bias and accuracy in judging sexism in mixed-gender social interactions

This research examined bias and accuracy in judging hostile and benevolent sexism during mixed-gender interactions. Bias is defined as underestimation or overestimation of a partner’s sexism. Accuracy is defined as covariation in two different ways, as (a) the strength of the association between a dyad member’s judgment and their partner’s sexism, across dyads, and (b) the ability to differentiate sexism between multiple targets. In Studies 1 and 2, members of mixed-gender dyads rated their own and their partners’ benevolent and hostile sexism. Overall, there was no covariation, across dyads, between perceptions and the partner’s self-reported sexism. However, women overestimated men’s hostile sexism; there was no evidence of biases for women judging men’s benevolent sexism. Men underestimated women’s hostile sexism and overestimated benevolent sexism. In Study 3, participants watched brief videos of male or female students (targets) from Study 1 and completed benevolent or hostile sexism items for each target as they thought the target would fill them out. Accuracy for detecting sexism across multiple targets (using sensitivity correlations) was significantly above chance for both forms of sexism. Male and female participants were more accurate at detecting hostile sexism in male targets than female targets. Participants were more accurate at detecting benevolent sexism of same-gender targets than opposite-gender targets. When judging targets of opposite gender, women’s judgments were significantly above chance for both forms of sexism, but men were not accurate for either forms of sexism. These studies suggest that there is bias and accuracy in first impression judgments of sexism.
Breast size as risk factor for tumor size at diagnosis.

BACKGROUND A prospective study was conducted to determine whether patients with larger breasts show larger tumors. MATERIALS AND METHODS 123 patients with primary breast cancer were evaluated (median follow-up 36 months). Breast size was determined as a reflection of cup size. RESULTS Cup size correlated with tumor diameter at diagnosis (p = 0.0038). On average, cup sizes were larger in postmenopausal than in premenopausal women (p = 0.0011), however, postmenopausal women did not show larger tumors than premenopausal. There was a significant positive correlation between body mass index, body weight and breast size (p < 0.0001). The mode of tumor detection (self vs. not self) was independent of breast size. No correlation was found between breast size and the patient's height, duration of breast feeding, smoking behavior or amount of alcohol consumption, hormone replacement therapy or use of oral contraceptives, number of involved lymph nodes or DFS and OS. CONCLUSION Patients with larger breasts showed larger tumors. The mode of tumor detection is independent of breast size.
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Evidence of prospective processes is increasingly common in psychological research, which suggests the fruitfulness of a theoretical framework for mind and brain built around future orientation. No metaphysics of determinism or indeterminism is presupposed by this framework, nor do considerations of scientific method require determinism—successful scientific theories in the natural sciences all involve probabilistic elements. We speculate that expressive behavior and moral decision making use prospective processes parallel to those used in nonmoral decisions.
Sources and implications of resonant mode splitting in silicon nanowire devices

This work investigates the effects of asymmetric cross-sectional geometry on the resonant response of silicon nanowires. The work demonstrates that dimensional variances of less than 2% qualitatively alter a nanosystem’s near-resonant response, yielding a non-Lorentzian frequency response structure, which is a direct consequence of resonant mode splitting. Experimental results show that this effect is independent of device boundary conditions, and can be easily modeled using continuous beam theory. Proper understanding of this phenomenon is believed to be essential in the characterization of the dynamic response of resonant nanowire systems, and thus the predictive design of such devices.
Predictive simulations and optimization of nanowire field-effect PSA sensors including screening

We apply our self-consistent PDE model for the electrical response of field-effect sensors to the 3D simulation of nanowire PSA (prostate-specific antigen) sensors. The charge concentration in the biofunctionalized boundary layer at the semiconductor–electrolyte interface is calculated using the propka algorithm, and the screening of the biomolecules by the free ions in the liquid is modeled by a sensitivity factor. This comprehensive approach yields excellent agreement with experimental current–voltage characteristics without any fitting parameters. Having verified the numerical model in this manner, we study the sensitivity of nanowire PSA sensors by changing device parameters, making it possible to optimize the devices and revealing the attributes of the optimal field-effect sensor.
Efficient Nonparametric Smoothness Estimation

Sobolev quantities (norms, inner products, and distances) of probability density functions are important in the theory of nonparametric statistics, but have rarely been used in practice, partly due to a lack of practical estimators. They also include, as special cases, $L^2$ quantities which are used in many applications. We propose and analyze a family of estimators for Sobolev quantities of unknown probability density functions. We bound the bias and variance of our estimators over finite samples, finding that they are generally minimax rate-optimal. Our estimators are significantly more computationally tractable than previous estimators, and exhibit a statistical/computational trade-off allowing them to adapt to computational constraints. We also draw theoretical connections to recent work on fast two-sample testing. Finally, we empirically validate our estimators on synthetic data.
Possible refinement of clinical thromboembolism assessment in patients with atrial fibrillation using echocardiographic parameters.

AIM Some transoesophageal echocardiogram (TEE) findings are associated with an increased risk of stroke in patients with atrial fibrillation (AF). This study was designed to evaluate and compare the accuracy of CHADS(2) and CHA(2)DS(2)-VASc in the prediction of these findings and test the additive value of transthoracic echocardiogram (TTE)-derived parameters as a possible refinement for these classifications. METHODS AND RESULTS Cross-sectional study of 405 consecutive patients who underwent TTE and TEE evaluation during AF. Stroke risk assessment was performed using the CHADS(2) and CHA(2)DS(2)-VASc scores, alone and alongside with the addition of two TTE-derived parameters (left atrium area and left ventricle global systolic function). Comparisons regarding the presence of left atrial appendage thrombi (LAA T), dense spontaneous echo contrast (SEC), and left atrial appendage (LAA) low flow velocities (LFV) were performed using receiver operating characteristic curves. In low-risk patients, as assessed through the CHA(2)DS(2)-VASc score and CHADS(2) and CHA(2)DS(2)-VASc scores plus echo parameters, no high-risk features were found on TEE. In subjects classified as low risk using CHADS(2), this figure rose to 10%. No significant differences were found between CHADS(2) and CHA(2)DS(2)-VASc in the prediction of LAA T, dense SEC, and LAA LFV. The addition of TTE-derived parameters to the previous clinical-risk scores resulted in improved prediction of the TEE endpoints. CONCLUSION These findings suggest that the use of TTE-derived parameters may be a valuable way of refining the available clinical risk schemes for the detection of surrogate markers of stroke. Follow-up studies using clinical endpoints will be necessary to confirm this hypothesis.
Post Milking Teat Dip Effect on Somatic Cell Count, Milk Production and Composition in Cows and Buffaloes

The effect of post milking teat dipping on somatic cell count (SCC) of milk was determined in 20 Crossbred cows and 20 Murrah buffaloes selected from institute's herd. The animals were divided into two groups of 10 each. Animals of Group I (control) were teat washed with water before the milking while Group II animals were applied teat dipping solution after the completion of milking. The cows were milked 3 times a day while buffaloes were milked twice a day. The milk samples were collected from control and treated animals on day 0, 5, 10, 15, respectively. The milk samples were analyzed for milk constituents like fat, protein, lactose, chloride, IgG, NEFA, pH and EC and total and differential somatic cell counts. The changes in milk composition and somatic cell counts were significantly different (p<0.01) between the animals and between the breeds. However SCC, chloride content (p<0.05) and epithelial cells (p<0.01) varied during different days of study. The alterations in SCC, epithelial cells, TLC, lymphocyte, neutrophil, IgG, and protein content were significantly different (p<0.01) between control and treated groups. The pH, EC, protein, SCC, epithelial cells, lymphocyte and neutrophil cells of milk declined significantly (p<0.05) after the application of teat dipping, the respective values were 6.5 vs 6.40, 2.28 vs 2.37 mhos, 3.33 vs 4.04%, 1.00 vs 0.87×10 5 cells/ml, 0.39 vs 0.34×10 5 cells/ml, 0.36 vs 0.31×1,000 cells/ml and 0.17 vs 0.14×1,000 cells/ml in cows. However in buffaloes, epithelial cells, lymphocytes, neutrophils, EC and SCC declined (p<0.05) after application of teat dipping, the values being 0.37 vs 0.29×10 5 cells/ml, 0.37 vs 0.25×1,000 cells/ml, 0.14 vs 0.11×1,000 cells/ml, 2.56 vs 2.37 mhos and 0.94 vs 0.73×10 5 cells/ml, respectively. The study indicated that post milking teat dipping could be used as an effective method for the lowering of SCC in milk of crossbred cows and buffaloes. (Asian-Aust. J. Anim. Sci. 2002. Vol 15, No. 10 : 1517-1522)
Inhibition of seagrass photosynthesis by ultraviolet-B radiation.

Effects of ultraviolet-B radiation on the photosynthesis of seagrasses (Halophila engelmanni Aschers, Halodule wrightii Aschers, and Syringodium filiforme Kütz) were examined. The intrinsic tolerance of each seagrass to ultraviolet-B, the presence and effectiveness of photorepair mechanisms to ultraviolet-B-induced photosynthetic inhibition, and the role of epiphytic growth as a shield from ultraviolet-B were investigated.Halodule was found to possess the greatest photosynthetic tolerance for ultraviolet-B. Photosynthesis in Syringodium was slightly more sensitive to ultraviolet-B while Halophila showed relatively little photosynthetic tolerance. Evidence for a photorepair mechanism was found only in Halodule. This mechanism effectively attenuated photosynthetic inhibition induced by ultraviolet-B dose rates and dosages in excess of natural conditions. Syringodium appeared to rely primarily on a thick epidermal cell layer to reduce photosynthetic damage. Halophila seemed to have no morphological or photorepair capabilities to deal with ultraviolet-B. This species appeared to rely on epiphytic and detrital shielding and the shade provided by other seagrasses to reduce ultraviolet-B irradiation to tolerable levels. The presence of epiphytes on leaf surfaces was found to reduce the extent of photosynthetic inhibition from ultraviolet-B exposure in all species.Observations obtained in this study seem to suggest the possibility of anthocyanin and/or other flavonoid synthesis as an adaptation to long term ultraviolet-B irradiation by these species. In addition, Halophila appears to obtain an increased photosynthetic tolerance to ultraviolet-B as an indirect benefit of chloroplast clumping to avoid photo-oxidation by intense levels of photosynthetically active radiation.
Automated QuantMap for rapid quantitative molecular network topology analysis

Summary: The previously disclosed QuantMap method for grouping chemicals by biological activity used online services for much of the data gathering and some of the numerical analysis. The present work attempts to streamline this process by using local copies of the databases and in-house analysis. Using computational methods similar or identical to those used in the previous work, a qualitatively equivalent result was found in just a few seconds on the same dataset (collection of 18 drugs). We use the user-friendly Galaxy framework to enable users to analyze their own datasets. Hopefully, this will make the QuantMap method more practical and accessible and help achieve its goals to provide substantial assistance to drug repositioning, pharmacology evaluation and toxicology risk assessment. Availability: http://galaxy.predpharmtox. org Contact: mats.gustafsson@medsci.uu. se or ola.spjuth@farmbio.uu. se Supplementary information: Supplementary data are available at Bioinformatics online.
Influence of Hydroxyethyl Starch on Healing of Colonic Anastomosis in a Rat Model of Peritonitis

Background: This study was designed to evaluate the role of different intravascular volume replacement regimens of HES 130/0.4 on wound healing process in left colonic anastomoses in the presence of intra-abdominal sepsis induced by murine model of cecal ligation and puncture (CLP). Methods: The left colonic anastomosis was performed in 40 rats that were divided into five groups (n = 8/group): saline controls (30 ml/kg); CLP plus saline (30 ml/kg); CLP plus HES (7.5, 15, or 30 ml/kg, respectively). Saline or HES was treated before the construction of left colonic anastomosis and on a regular daily basis. Anastomotic bursting pressures were measured in vivo on day 5. Tissue samples were obtained for analyses of hydroxyproline (HP) contents, myeloperoxidase (MPO) acivity, malondialdehyde (MDA), reduced glutathione (GSH) levels, and nuclear factor-κ B (NF-κ B) activation. The plasma levels of tumor necrosis factor (TNF)-α and interleukin (IL)-6 were also measured. Results: Intra-abdominal sepsis led to significant decreases in colonic anastomotic bursting pressures, and perianastomotic tissue HP contents and GSH levels, along with increases in perianastomotic tissue MPO activity, MDA levels and NF-κ B activation and plasma levels of TNF-α and IL-6. After treated with HES, these provoked perianastomotic tissue MPO activity, MDA levels, NF-κ B activation, and plasma levels of TNF-α and IL-6 were suppressed and GSH levels were restored, especially in 15 ml/kg HES group. Without obvious influence on systemic nutritional condition, HES 15 ml/kg but not HES 7.5 ml/kg significantly increased anastomotic bursting pressures, and perianastomotic tissue HP contents. However, HES 30 ml/kg even led to adverse effects on anastomotic bursting pressures. Conclusions: This study showed that moderate doses (15 ml/kg) of HES 130/0.4 administration significantly prevented this intraperitoneal sepsis-induced impaired anastomotic healing of the left colon. It also suggested the possibility of poorer anastomotic healing receiving HES at higher doses (30 ml/kg). Clearly, HES 130/0.4 now should not be recommended to use at a high doses postoperatively in sepsis.
Traumatic Events and Suicidal Behavior: Results From a National Mental Health Survey

The current study examined whether exposure to different types of traumatic events was differentially associated with suicidal ideation and attempts after adjusting for sociodemographic factors and presence of mental and physical disorders. Data came from the US National Comorbidity Survey Part II (N = 5877, aged 15–54 years, response rate: 82.4%) public use dataset. Interpersonal traumas and exposure to three or more types of traumatic events were particularly associated with suicidal behaviors. Age of onset analyses revealed that the age of traumatic exposure was earlier than the age at which suicidal behaviors began in the majority of respondents. The results imply that exposure to traumatic events is associated with the incidence of suicidal behaviors above and beyond the effect of sociodemographics, mental disorders, and physical disorders assessed in the survey. Clinicians and researchers need to be aware of these findings to determine early intervention programs.
Hydrogen Production by the Thermophilic Bacterium Thermotoga neapolitana

As the only fuel that is not chemically bound to carbon, hydrogen has gained interest as an energy carrier to face the current environmental issues of greenhouse gas emissions and to substitute the depleting non-renewable reserves. In the last years, there has been a significant increase in the number of publications about the bacterium Thermotoga neapolitana that is responsible for production yields of H2 that are among the highest achievements reported in the literature. Here we present an extensive overview of the most recent studies on this hyperthermophilic bacterium together with a critical discussion of the potential of fermentative production by this bacterium. The review article is organized into sections focused on biochemical, microbiological and technical issues, including the effect of substrate, reactor type, gas sparging, temperature, pH, hydraulic retention time and organic loading parameters on rate and yield of gas production.
In Vivo Molecular MRI Imaging of Prostate Cancer by Targeting PSMA with Polypeptide-Labeled Superparamagnetic Iron Oxide Nanoparticles

The prostate specific membrane antigen (PSMA) is broadly overexpressed on prostate cancer (PCa) cell surfaces. In this study, we report the synthesis, characterization, in vitro binding assay, and in vivo magnetic resonance imaging (MRI) evaluation of PSMA targeting superparamagnetic iron oxide nanoparticles (SPIONs). PSMA-targeting polypeptide CQKHHNYLC was conjugated to SPIONs to form PSMA-targeting molecular MRI contrast agents. In vitro studies demonstrated specific uptake of polypeptide-SPIONs by PSMA expressing cells. In vivo MRI studies found that MRI signals in PSMA-expressing tumors could be specifically enhanced with polypeptide-SPION, and further Prussian blue staining showed heterogeneous deposition of SPIONs in the tumor tissues. Taken altogether, we have developed PSMA-targeting polypeptide-SPIONs that could specifically enhance MRI signal in tumor-bearing mice, which might provide a new strategy for the molecular imaging of PCa.
The Learning Curve for Transradial Percutaneous Coronary Intervention Among Operators in the United States: A Study From the National Cardiovascular Data Registry

Background— Adoption of transradial percutaneous coronary intervention (TRI) in the United States is low and may be related to challenges learning the technique. We examined the relationships between operator TRI volume and procedural metrics and outcomes. Methods and Results— We used CathPCI Registry data from July 2009 to December 2012 to identify new radial operators, defined by an exclusively femoral percutaneous coronary intervention approach for 6 months after their first percutaneous coronary intervention in the database and ≥15 total TRIs thereafter. Primary outcomes of fluoroscopy time, contrast volume, and procedure success were chosen as markers of technical proficiency. Secondary outcomes included in-hospital mortality, bleeding, and vascular complications. Adjusted outcomes were analyzed by using operator TRI experience as a continuous variable with generalized linear mixed models. Among 54 561 TRI procedures performed at 704 sites, 942 operators performed 1 to 10 procedures, 942 operators performed 11 to 50 procedures, 375 operators performed 51 to 100 procedures, and 148 operators performed 101 to 200 procedures. As radial caseload increased, more TRIs were performed in women, in patients presenting with ST-segment elevation myocardial infarction, and for emergency indications. Decreased fluoroscopy time and contrast use were nonlinearly associated with greater operator TRI experience, with faster reductions observed for newer (<30–50 cases) compared with more experienced (>30–50 cases) operators. Procedure success was high, whereas mortality, bleeding, and vascular complications remained low across TRI volumes. Conclusions— As operator TRI volume increases, higher-risk patients are chosen for TRI. Despite this, operator proficiency improves with greater TRI experience, and safety is maintained. The threshold to overcome the learning curve appears to be approximately 30 to 50 cases.