Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of L-carnitine supplementation on growth performance, nutrient utilization, and nitrogen balance of broilers fed with animal fat

Aim: This experiment was conducted to evaluate the effect of L-carnitine supplementation on growth performance, nutrient utilization and nitrogen balance in broilers fed with animal fat. Materials and Methods: 80 day-old Cobb commercial broiler chicks were randomly assigned into two dietary treatment groups with four replicates of ten chicks each. The diets were isonitrogenous and isocaloric. The birds in both the control (T1) and treatment group (T2) were fed with a diet having 5% animal fat, while the treatment group (T2) was supplemented with 900 mg of L-carnitine. The birds were fed with standard broiler starter ration up to 4 weeks of age and finisher ration up to 6 weeks of age. Results: The average body weight (g), cumulative feed intake (g) and cumulative feed conversion ratio belonging to groups T1 and T2 at 6th week of age were 2091.25 and 2151.11, 3976.49 and 4171.68, 1.97 and 1.96 respectively. The percentage availability of the nutrients of two experimental rations T1 and T2 was 68.23 and 68.00 for dry matter, 58.72 and 55.98 for crude protein, 73.85 and 71.35 for ether extract, 34.19 and 33.86 for crude fiber, 79.18 and 79.59 for nitrogen free extract, 70.24 and 70.03 for energy efficiency and nitrogen balance (g/day) were 2.35 and 2.39, respectively. Conclusion: This study suggests that the supplementation of 900 mg L-carnitine in diet with added animal fat had no effect on growth performance, nutrient utilization, and nitrogen balance of broilers.
Classification of Differentials on Quantum Doubles and Finite Noncommutative Geometry

We discuss the construction of finite noncommutative geometries on Hopf algebras and finite groups in the `quantum groups approach'. We apply the author's previous classification theorem, implying that calculi in the factorisable case correspond to blocks in the dual, to classify differential calculi on the quantum codouble $D^*(G)=kG\lcocross k(G)$ of a finite group $G$. We give $D^*(S_3)$ as an example including its exterior algebra and lower cohomology. We also study the calculus on $D^*(\CA)$ induced from one on a general Hopf algebra $\CA$ in general and specialise to $D^*(G)=U(\cg)\lcocross k[G]$ as a noncommutative isometry group of an enveloping algebra $U(\cg)$ as a noncommutative space.
Cytoskeletal Alteration and Change of Retinal Nerve Fiber Layer Birefringence in Hypertensive Retina

ABSTRACT Purpose: Glaucoma damages the retinal nerve fiber layer (RNFL). Both RNFL thickness and retardance can be used to assess the damage, but birefringence, the ratio of retardance to thickness, is a property of the tissue itself. This study investigated the relationship between axonal cytoskeleton and RNFL birefringence in retinas with hypertensive damage. Materials and Methods: High intraocular pressure (IOP) was induced unilaterally in rat eyes. RNFL retardance in isolated retinas was measured. Cytostructural organization and bundle thickness were evaluated by confocal imaging of immunohistochemical staining of the cytoskeletal components: microtubules (MTs), F-actin, and neurofilaments. Bundles with different appearances of MT stain were studied, and their birefringence was calculated at different radii from the optic nerve head (ONH) center. Results: Forty bundles in eight normal retinas and 37 bundles in 10 treated retinas were examined. In normal retinas, the stain of axonal cytoskeleton was approximately uniform within bundles, and RNFL birefringence did not change along bundles. In treated retinas, elevation of IOP caused non-uniform alteration of axonal cytoskeleton across the retina, and distortion of axonal MTs was associated with decreased birefringence. The study further demonstrated that change of RNFL birefringence profiles along bundles can imply altered axonal cytoskeleton, suggesting that ultrastructural change of the RNFL can be inferred from clinical measurements of RNFL birefringence. The study also demonstrated that measuring RNFL birefringence profiles along bundles, instead of at a single location, may provide a more sensitive way to detect axonal ultrastructural change. Conclusions: Measurement of RNFL birefringence along bundles can provide estimation of cytoskeleton alteration and sensitive detection of glaucomatous damage.
Properties of integral membrane protein structures: Derivation of an implicit membrane potential

Distributions of each amino acid in the trans‐membrane domain were calculated as a function of the membrane normal using all currently available α‐helical membrane protein structures with resolutions better than 4 Å. The results were compared with previous sequence‐ and structure‐based analyses. Calculation of the average hydrophobicity along the membrane normal demonstrated that the protein surface in the membrane domain is in fact much more hydrophobic than the protein core. While hydrophobic residues dominate the membrane domain, the interfacial regions of membrane proteins were found to be abundant in the small residues glycine, alanine, and serine, consistent with previous studies on membrane protein packing. Charged residues displayed nonsymmetric distributions with a preference for the intracellular interface. This effect was more prominent for Arg and Lys resulting in a direct confirmation of the positive inside rule. Potentials of mean force along the membrane normal were derived for each amino acid by fitting Gaussian functions to the residue distributions. The individual potentials agree well with experimental and theoretical considerations. The resulting implicit membrane potential was tested on various membrane proteins as well as single trans‐membrane α‐helices. All membrane proteins were found to be at an energy minimum when correctly inserted into the membrane. For α‐helices both interfacial (i.e. surface bound) and inserted configurations were found to correspond to energy minima. The results demonstrate that the use of trans‐membrane amino acid distributions to derive an implicit membrane representation yields meaningful residue potentials. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Evaluation of the Hamburg model of couple therapy in the treatment of low sexual desire and vaginismus. A prospective group comparison

ABSTRACT The Hamburg model of sex therapy was evaluated in a number of studies until the beginning of the 1980s. For the “classic” sexual dysfunctions (e.g. orgasmic dysfunction, vaginismus, erectile dysfunction, and premature ejaculation), response rates of 75%–80% were reported. Later, the indication was extended to hypoactive sexual desire disorder (HSDD). However, less is known about the efficacy of the Hamburg model in the treatment of HSDD. In the present analyses, 22 pair treatments were evaluated, with the female subject suffering from either HSDD (12 pairs) or vaginismus (10 pairs). Treatments were carried out as intensive therapies (three weeks with daily sessions) between 1995 and 2011 at the Hamburg Institute for Sex Research and Forensic Psychiatry. In the statistical analyses, assessments from both therapists and patients were used and collected immediately before and after completion of treatment, as well as three months and approximately 1.5 years after the end of treatment. For vaginismus, similar results to those of previous studies were found. In contrast, catamnestic data indicated that women with HSDD showed poorer results in terms of sexual desire, satisfaction, and coitus frequency. Thus, women with HSDD may not benefit from the Hamburg model in the long run.
Characterization of the Specificity, Functionality, and Durability of Host T‐Cell Responses Against the Full‐Length Hepatitis E Virus

The interplay between host antiviral immunity and immunopathology during hepatitis E virus (HEV) infection determines important clinical outcomes. We characterized the specificity, functionality, and durability of host T‐cell responses against the full‐length HEV virus and assessed a novel “Quantiferon” assay for the rapid diagnosis of HEV infection. Eighty‐nine volunteers were recruited from Oxford, Truro (UK), and Toulouse (France), including 44 immune‐competent patients with acute HEV infection, 18 HEV‐exposed immunosuppressed organ‐transplant recipients (8 with chronic HEV), and 27 healthy volunteers. A genotype 3a peptide library (616 overlapping peptides spanning open reading frames [ORFs] 1‐3) was used in interferon‐gamma (IFN‐γ) T‐cell ELISpot assays. CD4+/CD8+ T‐cell subsets and polyfunctionality were defined using ICCS and SPICE analysis. Quantification of IFN‐γ used whole‐blood stimulation with recombinant HEV‐capsid protein in the QuantiFERON kit. HEV‐specific T‐cell responses were detected in 41/44 immune‐competent HEV exposed volunteers (median magnitude: 397 spot‐forming units/106 peripheral blood mononuclear cells), most frequently targeting ORF2. High‐magnitude, polyfunctional CD4 and CD8+ T cells were detected during acute disease and maintained to 12 years, but these declined over time, with CD8+ responses becoming more monofunctional. Low‐level responses were detectable in immunosuppressed patients. Twenty‐three novel HEV CD4+ and CD8+ T‐cell targets were mapped predominantly to conserved genomic regions. QuantiFERON testing demonstrated an inverse correlation between IFN‐γ production and the time from clinical presentation, providing 100% specificity, and 71% sensitivity (area under the receiver operator characteristic curve of 0.86) for HEV exposure at 0.3 IU/mL. Conclusion: Robust HEV‐specific T‐cell responses generated during acute disease predominantly target ORF2, but decline in magnitude and polyfunctionality over time. Defining HEV T‐cell targets will be important for the investigation of HEV‐associated autoimmune disease. (Hepatology 2016;64:1934‐1950).
Novel Sub-character HMM Models for Arabic Text Recognition

Hidden Markov Model (HMM) is one of the most widely used classifier for text recognition. In this paper we are presenting novel sub-character HMM models for Arabic text recognition. Modeling at sub-character level allows sharing of common patterns between different contextual forms of Arabic characters as well as between different characters. The number of HMMs gets reduced considerably while still capturing the variations in shape patterns. This results in a compact and efficient recognizer with reduced model set and is expected to be more robust to the imbalance in data distribution. Experimental results using the sub-character model based recognition of handwritten Arabic text as well printed Arabic text are reported.
Validation of memory accesses through symbolic analyses

The C programming language does not prevent out-of-bounds memory accesses. There exist several techniques to secure C programs; however, these methods tend to slow down these programs substantially, because they populate the binary code with runtime checks. To deal with this problem, we have designed and tested two static analyses - symbolic region and range analysis - which we combine to remove the majority of these guards. In addition to the analyses themselves, we bring two other contributions. First, we describe live range splitting strategies that improve the efficiency and the precision of our analyses. Secondly, we show how to deal with integer overflows, a phenomenon that can compromise the correctness of static algorithms that validate memory accesses. We validate our claims by incorporating our findings into AddressSanitizer. We generate SPEC CINT 2006 code that is 17% faster and 9% more energy efficient than the code produced originally by this tool. Furthermore, our approach is 50% more effective than Pentagons, a state-of-the-art analysis to sanitize memory accesses.
Large field-of-view movement-compensated intrinsic optical signal imaging for the characterization of the haemodynamic response to spreading depolarizations in large gyrencephalic brains

Haemodynamic responses to spreading depolarizations (SDs) have an important role during the development of secondary brain damage. Characterization of the haemodynamic responses in larger brains, however, is difficult due to movement artefacts. Intrinsic optical signal (IOS) imaging, laser speckle flowmetry (LSF) and electrocorticography were performed in different configurations in three groups of in total 18 swine. SDs were elicited by topical application of KCl or occurred spontaneously after middle cerebral artery occlusion. Movement artefacts in IOS were compensated by an elastic registration algorithm during post-processing. Using movement-compensated IOS, we were able to differentiate between four components of optical changes, corresponding closely with haemodynamic variations measured by LSF. Compared with ECoG and LSF, our setup provides higher spatial and temporal resolution, as well as a better signal-to-noise ratio. Using IOS alone, we could identify the different zones of infarction in a large gyrencephalic middle cerebral artery occlusion pig model. We strongly suggest movement-compensated IOS for the investigation of the role of haemodynamic responses to SDs during the development of secondary brain damage and in particular to examine the effect of potential therapeutic interventions in gyrencephalic brains.
Semantic patch inference

We propose a tool for inferring transformation specifications from a few examples of original and updated code. These transformation specifications may contain multiple code fragments from within a single function, all of which must be present for the transformation to apply. This makes the inferred transformations context sensitive. Our algorithm is based on depth-first search, with pruning. Because it is applied locally to a collection of functions that contain related changes, it is efficient in practice. We illustrate the approach on an example drawn from recent changes to the Linux kernel.
Epigenetic silencing of HNF1A associates with changes in the composition of the human plasma N-glycome

Protein glycosylation is a ubiquitous modification that affects the structure and function of proteins. Our recent genome wide association study identified transcription factor HNF1A as an important regulator of plasma protein glycosylation. To evaluate the potential impact of epigenetic regulation of HNF1A on protein glycosylation we analyzed CpG methylation in 810 individuals. The association between methylation of four CpG sites and the composition of plasma and IgG glycomes was analyzed. Several statistically significant associations were observed between HNF1A methylation and plasma glycans, while there were no significant associations with IgG glycans. The most consistent association with HNF1A methylation was observed with the increase in the proportion of highly branched glycans in the plasma N-glycome. The hypothesis that inactivation of HNF1A promotes branching of glycans was supported by the analysis of plasma N-glycomes in 61 patients with inactivating mutations in HNF1A, where the increase in plasma glycan branching was also observed. This study represents the first demonstration of epigenetic regulation of plasma glycome composition, suggesting a potential mechanism by which epigenetic deregulation of the glycome may contribute to disease development.
Endogenous Peptide Discovery of the Rat Circadian Clock

Understanding how a small brain region, the suprachiasmatic nucleus (SCN), can synchronize the body's circadian rhythms is an ongoing research area. This important time-keeping system requires a complex suite of peptide hormones and transmitters that remain incompletely characterized. Here, capillary liquid chromatography and FTMS have been coupled with tailored software for the analysis of endogenous peptides present in the SCN of the rat brain. After ex vivo processing of brain slices, peptide extraction, identification, and characterization from tandem FTMS data with <5-ppm mass accuracy produced a hyperconfident list of 102 endogenous peptides, including 33 previously unidentified peptides, and 12 peptides that were post-translationally modified with amidation, phosphorylation, pyroglutamylation, or acetylation. This characterization of endogenous peptides from the SCN will aid in understanding the molecular mechanisms that mediate rhythmic behaviors in mammals.
Intelligent User Interface Tools

This paper describes an analysis tool for dynamic gaming env ironments. It is based on an image processing system and a conting e cy analysis tool for extracting the rules that the user is applying in a drivin g game simulation. The tool is intended for a cognitive modelling architecture tha t will learn from the user’s previous actions to minimize the amount of assumptio ns made to control the environment. Interaction with the dynamically changin g visual environments at real-time is important. This paper discusses our initial attempt to analyze dynamic gaming environments through statistical measures, o ur learning goal from previous experiences, the limitations, and its implicatio ns for user interface environments that dynamically change.
Efficacy and Safety of Insulin Degludec versus Insulin Glargine: A Systematic Review and Meta-Analysis of Fifteen Clinical Trials

Aims Insulin degludec (IDeg) and insulin glargine (IGlar) are both proved to be effective in diabetes. This study aimed to assess the effects and safety of IDeg versus IGlar. Methods A systematic literature search was conducted using the PubMed, EMBASE, and Cochrane Library electronic databases to identify all randomized controlled trials (RCTs). Results Fifteen RCTs were identified. The combined data showed that the decrease in the glycosylated hemoglobin (HbA1c) level was slightly different, and the proportion of patients who achieved HbA1c < 7% was similar between the IDeg and IGlar groups. Further, a statistically significant decrease in the fasting plasma glucose level was observed in the IDeg group as compared to the IGlar group. In patients with T2DM, IDeg was associated with lower rates of overall hypoglycemia. Nocturnal hypoglycemia was significantly lower in the case of IDeg than in the case of IGlar in both T1DM and T2DM patients. No statistically significant differences were observed between the groups. Conclusions Compared with IGlar, IDeg is associated with equivalent glycemic control and a statistically significantly lower rate of nocturnal hypoglycemia in patients with T1DM and T2DM. In T2DM patients, IDeg also provides better results in terms of overall hypoglycemia.
Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling

Gravity models have a long history of use in describing and forecasting the movements of people as well as goods and services, making them a natural basis for disease transmission rates over distance. In agent-based micro-simulations, gravity models can be directly used to represent movement of individuals and hence disease. In this paper, we consider a range of gravity models as fits to movement data from the UK and the US. We examine the ability of synthetic networks generated from fitted models to match those from the data in terms of epidemic behaviour; in particular, times to first infection. For both datasets, best fits are obtained with a two-piece ‘matched’ power law distance distribution. Epidemics on synthetic UK networks match well those on data networks across all but the smallest nodes for a range of aggregation levels. We derive an expression for time to infection between nodes in terms of epidemiological and network parameters which illuminates the influence of network clustering in spread across networks and suggests an approximate relationship between the log-likelihood deviance of model fit and the match times to infection between synthetic and data networks. On synthetic US networks, the match in epidemic behaviour is initially poor and sensitive to the initially infected node. Analysis of times to infection indicates a failure of models to capture infrequent long-range contact between large nodes. An assortative model based on node population size captures this heterogeneity, considerably improving the epidemiological match between synthetic and data networks.
The computational power of matchgates and the XY interaction on arbitrary graphs

Matchgates are a restricted set of two-qubit gates known to be classically simulable when acting on nearest-neighbor qubits on a path, but universal for quantum computation when the qubits are arranged on certain other graphs. Here we characterize the power of matchgates acting on arbitrary graphs. Specifically, we show that they are universal on any connected graph other than a path or a cycle, and that they are classically simulable on a cycle. We also prove the same dichotomy for the XY interaction, a proper subset of matchgates related to some implementations of quantum computing.
Phase I study of low-dose suramin as a chemosensitizer in patients with advanced non-small cell lung cancer.

PURPOSE Our preclinical studies have shown that acidic and basic fibroblastic growth factors confer broad spectrum chemoresistance and that low concentrations (10-50 microM) of suramin, a nonspecific fibroblastic growth factor inhibitor, enhance the antitumor activity of paclitaxel in vivo. The present Phase I study evaluated low-dose suramin in combination with paclitaxel/carboplatin in advanced non-small cell lung cancer patients. EXPERIMENTAL DESIGN Patients received suramin followed by paclitaxel (175-200 mg/m(2)) and carboplatin area under the concentration-time curve of 6 mg/ml/min, every 3 weeks. The initial suramin dose for the first cycle was 240 mg/m(2), and the doses for subsequent cycles were calculated based on the 72-h pretreatment plasma concentrations. The recommended suramin dose would yield plasma concentrations of 10-20 microM at 48 h in >or=5 of 6 patients. RESULTS Fifteen patients (11 stage IV, 4 stage IIIB, 9 chemonaive, and 6 previously treated) received 85 courses. The most common toxicities were neutropenia, nausea/vomiting, malaise/fatigue, and peripheral neuropathy. No treatment-related hospitalizations, adrenal dysfunction, or episodes of sepsis occurred. The initial suramin dose resulted in the targeted concentrations of 10-20 microM at 48 h in 5 of the first 6 patients treated but also resulted in peak concentrations > 50 microM in all patients. Dividing the suramin dose to be administered in two doses, 24 h apart, yielded the target concentrations and avoided undesirable peak concentrations. Discernable antitumor activity occurred in 7 of 10 patients with measurable disease, including 2 with prior chemotherapy. The median time to tumor progression is 8.5 months (range, 3-27+ months) for 12 evaluable patients. CONCLUSIONS Low-dose suramin does not increase the toxicity of paclitaxel/carboplatin combination. The suramin dose can be calculated based on clinical parameters. Because of the preliminary antitumor activity observed, efficacy studies in chemonaive and chemorefractory patients are under way.