Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved flexible refinement of protein docking in CAPRI rounds 22–27

Since the fourth evaluation for critical assessment of prediction of interactions (CAPRI), we have made improvements in three major areas in our refinement approach, namely the treatment of conformational flexibility, the binding free energy model, and the search algorithm. First, we incorporated backbone flexibility into our previous approach, which only optimized rigid backbone poses with limited side‐chain flexibility. Here, we formulated and solved the conformational search as a hierarchical optimization problem (involving rigid‐body poses, backbone flexibility, and side‐chain flexibility). Second, we used continuum electrostatic calculations to include solvation effects in the binding free energy model. Finally, we eliminated sloppy modes (directions in which the free energy is essentially constant) to improve the efficiency of the search. With these improvements, we produced correct predictions for 6 of the 10 latest CAPRI targets, including one high, three medium, and two acceptable accuracy predictions. Compared to our previous performance in CAPRI, substantial improvements have been made for targets requiring homology modeling. Proteins 2013; 81:2129–2136. © 2013 Wiley Periodicals, Inc.
Lorentzian quantum cosmology

We argue that the Lorentzian path integral is a better starting point for quantum cosmology than its Euclidean counterpart. In particular, we revisit the minisuperspace calculation of the Feynman path integral for quantum gravity with a positive cosmological constant. Instead of rotating to Euclidean time, we deform the contour of integration over metrics into the complex plane, exploiting Picard-Lefschetz theory to transform the path integral from a conditionally convergent integral into an absolutely convergent one. We show that this procedure unambiguously determines which semiclassical saddle point solutions are relevant to the quantum mechanical amplitude. Imposing ``no-boundary'' initial conditions, i.e., restricting attention to regular, complex metrics with no initial boundary, we find that the dominant saddle contributes a semiclassical exponential factor which is precisely the inverse of the famous Hartle-Hawking result.
Effect of dietary supplementation of Mycofix® secure on milk production and its constituents in lactating crossbred cows.

A study was conducted to determine the effect of dietary supplementation of sodium bentonite a mycotoxin binder (Mycofix® secure, Biomin, Singapore) on milk production and milk constituents including somatic cell count and aflatoxin M1 level in lactating crossbred cows. Total ninety cows of three farms were selected and randomly divided into treatment and control group on each farm on the basis of stage of lactation and milk yield. The feeding practices followed, though vary between farms, were common in both the groups. Animals of treatment group received additional sodium bentonite @ 15 g/animal/day for 30 days. There was no significant difference in milk yield, or milk fat, SNF and protein content of milk between two groups on any of the three farms. The somatic cell count (SCC), however, decreased significantly in treatment group on two farms. Among three farms, aflatoxin M1 (AFM1) level also reduced in treatment group on all farms. The result revealed that dietary supplementation of sodium bentonite (Mycofix® secure) was effective in reducing SCC and AFM1 content of milk.
Multiple developmental roles of VEGF suggested by a LacZ-tagged allele.

Vascular endothelial growth factor (VEGF) is an angiogenic factor and a potent stimulator of microvascular permeability. It is a mitogen specific for endothelial cells. The expression of VEGF and its two receptors, Flk-1 and Flt-1, is pivotal for the proper formation of blood vessels in embryogenesis as shown by gene-targeting experiments. Interestingly, the loss of even a single allele of VEGF led to embryonic lethality between day E9.5 and day E10.5 in the mouse. To assess the role of VEGF during embryonic development we decided to tag VEGF expression with LacZ, by inserting an IRES (internal ribosome entry site)-LacZ reporter cassette into the 3' untranslated region of the gene. This alteration enabled us to monitor VEGF expression throughout embryonic development at single-cell resolution. beta-Galactosidase expression from the altered VEGF locus was first observed prior to gastrulation and was detectable at all stages of vascular development in the embryo. Later, the specific cellular distribution and the level of VEGF expression indicated its pleiotropic role in development. High expression levels seemed to be associated with vasculogenesis and permeability, whereas lower levels were associated with angiogenesis and cell migration. In addition, we found VEGF expression in a subtype of endothelial cells present in the endocardium. We believe that the LacZ-tagged allele we have generated offers a precise means of detecting VEGF expression under a variety of physiological and pathological conditions.
Performance Analysis of Professional, Semiprofessional, and Junior Elite Rugby League Match-Play Using Global Positioning Systems

Abstract McLellan, CP and Lovell, DI. Performance analysis of professional, semiprofessional, and junior elite rugby league match-play using global positioning systems. J Strength Cond Res 27(12): 3266–3274, 2013—The aim of the present study was to examine the positional differences in physical performance measures of professional, semiprofessional, and junior elite rugby league match-play using portable Global Positioning Systems (GPSs). Twelve professional, 12 semiprofessional, and 18 junior elite male rugby league players were monitored during 5 regular-season competition matches using portable GPS software. The mean total distance traveled during professional (8,371 ± 897 m) and semiprofessional (7,277 ± 734 m) match-play was significantly (p < 0.05) greater than that traveled during elite junior (4,646 ± 978 m) match-play. Position-specific total distance traveled and distance traveled per minute of playing time were significantly (p < 0.05) less for junior elite backs (5,768 ± 765 m; 74 ± 11 m·min−1) and forwards (4,774 ± 564 m; 82 ± 5 m·min−1) in comparison to those in professional (backs: 8,158 ± 673 m; 101 ± 8 m·min−1 and forwards: 8,442 ± 812 m; 98 ± 12 m·min−1) and semiprofessional (backs: 7,505 ± 765 m; 94 ± 8 m·min−1 and forwards: 6,701 ± 678 m; 89 ± 8 m·min−1) match-play. Maximum running speed, maximum sprints, and total sprint distance traveled by professional players were all significantly (p < 0.05) greater than those traveled by junior elite players but not semiprofessional players during match-play. Professional backs and forwards performed significantly (p < 0.05) more maximum sprints and traveled greater total distance during match-play in comparison to semiprofessional and junior elite players. The present findings demonstrate minimal differences in the physical performance measures of professional and semiprofessional rugby league match-play. The position-specific performance characteristics of junior elite match-play indicate that current junior elite player-development pathways may not provide adequate preparation for players transitioning into professional competition.
Apparent diffusion coefficient mapping of salivary gland tumors: prediction of the benignancy and malignancy.

BACKGROUND AND PURPOSE Preoperative prediction of tumor malignancy is clinically very important, because this information strongly influences the surgical plan. We evaluate the preoperative apparent diffusion coefficient (ADC) maps of benign and malignant salivary gland tumors. MATERIALS AND METHODS High-resolution MR imaging was performed on 31 patients with benign or malignant salivary gland tumors; ADC maps of the tumors were also obtained. Surface coils of 47 or 110 mm diameter were used to improve the image resolution. The ADCs were compared with histologic features of the excised tumors. RESULTS The ADC maps effectively depicted the histologic features of the salivary gland tumors, such as presence of cancer cells, myxomatous tissues, fibrosis, necrosis, cyst formation, and lymphoid tissues. The ADC maps showed that more frequent areas with high ADCs (> or = 1.8 x 10(-3) mm(2)/s) were significantly greater in benign tumors than in malignant tumors. The sensitivity and specificity for high ADC occupying fewer than 5% of the area of a tumor was 89% and 100%, respectively, resulting in 97% accuracy, 100% positive predictive value, and 96% negative predictive value. CONCLUSION The ADC may provide preoperative tissue characterization of the salivary gland tumors.
Papillary Squamous Cell Carcinoma, Not Otherwise Specified (NOS) of the Penis: Clinicopathologic Features, Differential Diagnosis, and Outcome of 35 Cases

There is a group of low-grade papillomatous squamous cell carcinomas (SCC) of the penis, collectively designated as “verruciform,” that are difficult to classify. A proposal of classification grouped these tumors in warty (condylomatous), verrucous, and papillary carcinomas. Papillary SCC, not otherwise specified is the third distinctive type of penile low-grade verruciform neoplasms. We are presenting clinicopathologic features of 35 cases from 2 institutions. All specimens were penectomies or circumcisions. Mean age was 57 years. Sites of involvement were glans alone in 18 cases (51%), glans, coronal sulcus and foreskin in 13 cases (37%), glans and sulcus in 3 cases (9%), and foreskin in 1 case (3%). Papillary carcinomas were large (mean 5.6 cm) exophytic low-grade squamous neoplasms with hyperkeratosis and papillomatosis. Papillae were variable in length and shape. The tip was straight, undulated, spiky, or blunt. There was no koilocytosis. The interface between tumor and stroma was characteristically jagged and a moderate stromal reaction was evident in most cases. The majority of the tumors (94%) showed a low-grade histology with focally present poorly differentiated areas in 6% of the cases. The mean thickness of the tumor was 9.4 mm. The most commonly invaded anatomic levels were the corpus spongiosum and/or dartos (77% cases). Corpus cavernosum was invaded in 8 cases (23%). Vascular and perineural invasion were unusual. Frequent associated lesions were squamous hyperplasia, differentiated penile intraepithelial neoplasia, and lichen sclerosus (74%, 46%, and 34%, respectively). Nodal metastases were identified in 3 of 12 patients with bilateral groin dissections. Of the 20 patients followed, 18 were either with no evidence of disease (15 cases) or died from unrelated causes (3 cases). One patient was alive with evidence of systemic metastases and 1 died from disseminated penile cancer 32 months after original penectomy. In conclusion, papillary carcinomas were exophytic albeit, often deeply invasive low-grade neoplasms, with a low rate of nodal metastasis characterized by complex papillae, irregular fibrovascular cores, and jagged tumor base. Papillary SCC should be distinguished from other penile verruciform tumors, including verrucous and variants, warty and papillary basaloid carcinomas, and carcinoma cuniculatum. Helpful morphologic features for differential diagnosis are provided.
Fibrillation is More Complex in the Left Ventricle than in the Right Ventricle

VF Patterns in the Right and Left Ventricles. Introduction: The mechanisms that maintain ventricular fibrillation (VF) are not completely understood. It has been proposed that increased ventricular wall thickness destabilizes VF wavefronts and therefore is an important determinant of VF activation patterns. We hypothesized that if this is the case, then VF patterns on the thin‐walled right ventricle (RV) should he simpler than those on the thick‐walled left ventricle (LV).
Implementation von Arbeitsbeschaffungsmaßnahmen (ABM) in den neuen Bundesländern: Erfahrungen, Probleme, Forschungsbedarf

"In dem Beitrag wird uber bisher gewonnene Erfahrungen bei der Implementation von Arbeitsbeschaffungsmasnahmen in den neuen Bundelandern berichtet. Am Beispiel der Mittelbereitstellung fur ABM wird zunachst gezeigt, wie Rahmenbedingungen ihre Planung und Durchfuhrung beeinflussen konnen. Durch Verstetigung in der Vorbereitung der Masnahmen und ihrer Finanzierung lassen sich organisations- und ablaufbedingte time lags sowie hektische und damit im allgemeinen uneffektive Masnahmeaquisitionen verhindern bzw. weitgehend einschranken. Hauptakteure im unmittelbaren Implemantationsprozes sind das Arbeitsamt und die Masnahmetrager. Ihre Integration und dabei zutage tretende Probleme bilden den Schwerpunkt des Beitrages. Auf der Grundlage einer vom Brandenburgischen Institut fur Arbeitsmarkt und Beschaftigung (biab) im Auftrag der Bundesanstalt fur Arbeit durchgefuhrten Befragung von ABM-Teilnehmern werden Fragen der Organisation und Effektivitat bei der Durchfuhrung von ABM angesprochen. Angesichts der gegebenen Haushaltslage und betriebswirtschaftlicher Kalkule der Masnahmetrager, aber auch im Interesse der Masnahmeteilnehmer, sind bei der Planung und Durchfuhrung von ABM zunehmend qualitative Kriterien zugrunde zu legen. Unter anderem auch hierzu besteht weiterer Forschungsbedarf. " (Autorenreferat, IAB-Doku)
Recent advances in diagnosis and therapy of human papillomaviruses

Infection with human papillomavirus is extremely common throughout the world. Almost 50% of sexually active young women are infected with human papillomavirus and although most infections are transient, a subset has the potential to progress to invasive cancer. During the last 20 years, our understanding of the human papillomavirus life cycle and the role of human papillomavirus in human cancer has dramatically increased. Recent technological advances in human papillomavirus detection have provided the means to detect the presence of human papillomavirus with great sensitivity. In the context of patient care, there is still substantial debate regarding the optimal diagnostic and prognostic use of information derived from hybrid capture or polymerase chain reaction-based detection. The inventory of available treatment options is growing somewhat slowly. The most promising advances are being made in the clinical evaluation of candidates for prophylactic vaccination. This review is focused on the current status and future directions of prevention, diagnosis and therapy.
In Vitro Studies on the Effect of Dialysis Solutions on Peritoneal Leukocytes

Within the limitations of the various experimental protocols there appears to be agreement in the literature that unused dialysis fluids, at least when studied in vitro, adversely affect multiple leukocyte functions. The effects of dialysis fluids on leukocytes that have been reported to date include: 1. Decreased cell viability of PMNs, PM phis, PBMCs, and lymphocytes; 2. Inhibited phagocytosis and bacterial killing of various microorganisms by PM phis, PMNs, and peripheral blood leukocytes; 3. Reduced secretion of leukotrienes (LTB4, LTC4) from peritoneal and peripheral blood PMNs and PBMCs; 4. Reduced secretion of prostaglandins (PGE2, TXB2 and 6-keto-PGF1 alpha) from PM phi; 5. Decreased production of many cytokines including TNF alpha, IL-8, and IL-6 in PM phis and PBMCs. In addition, several studies targeting the potential mechanisms by which dialysis solutions inhibit leukocyte function identified the initial low pH of the fluids in combination with their lactate content as being of primary relevance, since they may lead to a rapid intracellular acidification of leukocytes. Moreover, some studies indicated the importance of fluid hyperosmolarity and excessive glucose concentrations. These results are indirectly supported by recent in vitro investigations of alternative fluids, which showed improved leukocyte function following exposure to solutions with neutral pH, bicarbonate buffer instead of lactate, or normal osmolarity due to use of an alternative osmotic agent (e.g., glucose polymer). In conclusion, the evidence obtained during in vitro experimentation suggests that current dialysis fluids are, indeed, not biocompatible. However, whether this also bears physiological relevance in vivo remains to be established in controlled clinical trials comparing conventional fluids to alternative solutions with improved biocompatibility. With regard to the future development of in vitro models for biocompatibility assessment, the following guidelines are suggested: 1. Cell functional parameters should be studied in more than one cell population; 2. Depending on which fluid aspect is under investigation, short or even very short exposure times should be used (e.g., < 30 min for pH/buffer studies; < 4 hours for osmolality/osmotic agent studies); 3. In case the parameter/readout of interest requires longer study periods than indicated above (e.g., studies of cytokine induction or surface receptor expression), preincubation/recovery models should be preferred over coincubation experiments.
SOME INCONVENIENT TRUTHS ABOUT SEX CHROMOSOME DOSAGE COMPENSATION AND THE POTENTIAL ROLE OF SEXUAL CONFLICT

Sex chromosome dosage compensation was once thought to be required to balance gene expression levels between sex‐linked and autosomal genes in the heterogametic sex. Recent evidence from a range of animals has indicated that although sex chromosome dosage compensation exists in some clades, it is far from a necessary companion to sex chromosome evolution, and is in fact rather rare in animals. This raises questions about why complex dosage compensation mechanisms arise in some clades when they are not strictly needed, and suggests that the role of sex‐specific selection in sex chromosome gene regulation should be reassessed. We show there exists a tremendous diversity in the mechanisms that regulate gene dosage and argue that sexual conflict may be an overlooked agent responsible for some of the variation seen in sex chromosome gene dose regulation.
Sphingosine 1‐phosphate receptor modulators: a new class of immunosuppressants

Abstract: In this review, we summarize how FTY720 came from the lab bench to the bedside by examining its structural similarities to natural occuring sphingosine analogues, the mechanism of action, and clinical applicability to not only transplantation but also autoimmune, oncological, and neurobiological fields. FTY720, a sphingosine 1‐phosphate (S1P) analogue, promotes the survival of human and animal allografts by sequestering T lymphocytes within peripheral lymphoid tissue. The mechanism of sequestration is three‐fold:(1) T lymphocytes are driven into peripheral lymph nodes in a chemokine dependent manner by FTY720;(2) FTY720 downregulates sphingosine 1‐phosphate receptors (S1PRs) on the T lymphocyte surface, rendering it unable to migrate along a S1P gradient; and (3) FTY720 closes stromal gates on the abluminal side of the lymphatic endothelium. Future areas of investigation include developing S1P analogues that have specific agonist binding to S1PRs avoiding side effects seen in non‐specific binding.
DIAGNOSIS OF MILK FEVER BY A WATER HARDNESS TEST KIT IN EWES

The aim of the study was to evaluate the measurement of total calcium levels in sera of sheep with and without milk fever by using a commercial water hardness test kit. Thirty sheep with findings of milk fever from 9 different farms were used in the present study. Total serum calcium concentrations were determined by using a commercial water hardness test kit and a laboratory automated biochemical analyzer. Results of the test kit and laboratory methods were significantly (P < 0.001) correlated (Spearman’s p = 0.896). In conclusion, it has been determined that total calcium levels in sheep sera may be determined with a water hardness test kit as used in this study, and that data are in concordance with the clinical findings and the other laboratory results.
Arginine (Arg) Turnover and Oxidation in Neonates Receiving Total Parenteral Nutrition (TPN) • 1497

In human, Arg is generally considered a dispensable amino acid. However, it has been proposed that Arg may be an indispensable amino acid in neonates after an increase in blood ammonia level was observed when arginine was removed from amino acid solution used in parenteral nutrition.Method: In order to estimate net de novo synthesis, in vivo, in neonates fed parenterally, I evaluated Arg and citrulline (Cit) metabolism measuring respective plasma amino acids fluxes and whole-body rate of Arg oxidation based on a single pool model (Beaumier, 1995). Rate of conversion of plasma Cit to Arg was also measured using the Clarke and Bier equation (1982). Protein turnover was also measured usingα-ketoisocaproic acid (α-KIC) as representative metabolite of leucine metabolism (Matthews 1982). Experiments: After being on TPN for 4-5 days, providing 3 gm of protein/kg/day and a minimum of 120 kcal/kg/day, a known primed constant infusion of [5-13C] Arg,[15N2-guanidino] Arg, [5,5-2H2, 13C-ureido] Cit and [5,5,5-2H2] leucine was given for five hours. Blood and breath samples were taken once before and twice, at 30 minute intervals, at the end of the infusion. Expired 13CO2 was corrected for under-recovery of 13C-label from infused [5-13C] ornithine. Isotopic abundance of amino acids and α-KIC was measured by GC/MS as methyl ester-TFA and t-BDMS derivatives, respectively. Results: Under these conditions, plasma Arg and Cit flux were measured at 209 ± 17 and 37± 3 μmol/kg/h, respectively. Arg oxidation was measured at 76± 6 with a dietary Arg intake was 69 ± 10 μmol/kg/h. Rate of conversion of plasma Cit into Arg was 15 ± 3 μmol/kg/h. The small excess in Arg oxidation and the low rate of conversion support the concept that neonates have a very limited rate of Arg de novo synthesis. Leucine appearance from protein breakdown was 141 ± 18 μmol/kg/h, which represents 9.4 ± 1.2 g/kg/day of protein. Conclusion: Net rate of endogenous Arg synthesis is measurable in neonates receiving TPN but remains relatively small in comparison to the whole-body turnover of the amino acid. These results are consistent with a limiting capacity for neonates to synthesize arginine supporting the recommendation that Arg is an indispensable amino acid in neonates fed a parenteral solution.
Magnetic Fields at Uranus

The magnetic field experiment on the Voyager 2 spacecraft revealed a strong planetary magnetic field of Uranus and an associated magnetosphere and fully developed bipolar masnetic tail. The detached bow shock wave in the solar wind supersonic flow was observed upstream at 23.7 Uranus radii (1 RU = 25,600 km) and the magnetopause boundary at 18.0 RU, near the planet-sun line. A miaximum magnetic field of 413 nanotesla was observed at 4.19 RU , just before closest approach. Initial analyses reveal that the planetary magnetic field is well represented by that of a dipole offset from the center of the planet by 0.3 RU. The angle between Uranus' angular momentum vector and the dipole moment vector has the surprisingly large value of 60 degrees. Thus, in an astrophysical context, the field of Uranus may be described as that of an oblique rotator. The dipole moment of 0.23 gauss R3U, combined with the large spatial offset, leads to minimum and maximum magnetic fields on the surface of the planet of approximately 0.1 and 1.1 gauss, respectively. The rotation period of the magnetic field and hence that of the interior of the planet is estimated to be 17.29� 0.10 hours; the magnetotail rotates about the planet-sun line with the same period. Thelarge offset and tilt lead to auroral zones far from the planetary rotation axis poles. The rings and the moons are embedded deep within the magnetosphere, and, because of the large dipole tilt, they will have a profound and diurnally varying influence as absorbers of the trapped radiation belt particles.