Miracle-dz/UniFAR-FTUs huggingface dataset:
Sparse Gaussian graphical model with missing values

Recent advances in measurement technology have enabled us to measure various omic layers, such as genome, transcriptome, proteome, and metabolome layers. The demand for data analysis to determine the network structure of the interaction between molecular species is increasing. The Gaussian graphical model is one method of estimating the network structure. However, biological omics data sets tend to include missing values, which is conventionally handled by preprocessing. We propose a novel method by which to estimate the network structure together with missing values by combining a sparse graphical model and matrix factorization. The proposed method was validated by artificial data sets and was applied to a signal transduction data set as a test run.
The Vehicle Routing Problem with Time Windows Part I: Tabu Search

This paper describes a tabu search heuristic for the vehicle routing problem with time windows. The tabu search is based on specialized local search heuristics that maintain the feasibility of the solution at all time. Computational results on a standard set of test problems are reported, as well as comparisons with other heuristics.
Current management of secondary hyperparathyroidism: a multicenter observational study (COSMOS).

STUDY AIMS To survey bone mineral disturbances in the hemodialysis (HD) population in Europe and current clinical practice in Europe for the prevention, diagnosis and treatment of secondary hyperparathyroidism (SHPT) in HD patients. PRIMARY OBJECTIVES First, to estimate the prevalence of Kidney Disease Outcomes Quality Initiative (K/DOQI) guideline achievement in a representative sample of European hemodialysis subjects. As part of this objective, we will investigate the prevalence of achievement by type of dialysis, type of center and time on dialysis (less than or greater than 1 year). Among new dialysis subjects (less than 1 year), we will evaluate prevalence of K/DOQI target achievement until the end of the study. The study will run for 3 years. Second, to estimate the association of bone mineral markers (parathyroid hormone [PTH], calcium [Ca], serum phosphorus [P] and calcium phosphate product [CaxP]) classified by achievement of K/DOQI targets with mortality and overall cardiovascular hospitalization. Third, to characterize the longitudinal changes in bone mineral markers. As part of this objective, we will describe the patterns and predictors of bone mineral markers and achievement, with K/DOQI targets, using repeated measurements on individuals over time. SECONDARY OBJECTIVES First, To estimate the association of bone mineral markers (PTH, Ca, P and CaxP) classified by achievement of K/DOQI targets with specific cardiovascular outcomes, parathyroidectomy, manifest bone disease (including incidence of symptomatic bone fractures), hospitalizations and vascular access. Second, to evaluate the additional value of albumin and hemoglobin levels in conjunction with bone mineral markers in the prediction of mortality and clinical events.
Identification of a fibronectin‐binding domain within the Campylobacter jejuni CadF protein

The binding of Campylobacter jejuni to fibronectin (Fn), a component of the extracellular matrix, is mediated by a 37 kDa outer membrane protein termed CadF for Campylobacter adhesion to Fn. Previous studies have indicated that C. jejuni binds to Fn on the basolateral surface of T84 human colonic cells. To further characterize the interaction of the CadF protein with Fn, enzyme‐linked immunosorbent assays were performed to identify the Fn‐binding domain (Fn‐BD). Using overlapping 30‐mer and 16‐mer peptides derived from translated cadF nucleotide sequence, maximal Fn‐binding activity was localized to four amino acids (AA 134–137) consisting of the residues phenylalanine‐arginine‐leucine‐serine (FRLS). A mouse α‐CadF peptide polyclonal antibody (M α‐CadF peptide pAb) was generated using FRLS containing peptides and found to react with viable C. jejuni as judged by indirect fluorescent microscopy, suggesting that the FRLS residues are surface‐exposed. Binding of CadF to purified Fn and INT 407 human epithelial cells was significantly inhibited with peptides containing the Fn‐BD. Moreover, a CadF recombinant variant protein, in which the Phe‐Arg‐Leu residues (CadF AA 134–136) were altered to Ala‐Ala‐Gly, exhibited a 91% decrease in Fn‐binding activity as compared with the wild‐type CadF protein. Collectively, these data indicate that the FRLS residues (CadF AA 134–137) of the C. jejuni CadF protein possess Fn‐binding activity.
Chronic repetitive transcranial magnetic stimulation increases hippocampal neurogenesis in rats

Aim: While the underlying therapeutic mechanisms of repetitive transcranial magnetic stimulation (rTMS) treatment for depression remain unclear, recent animal studies have suggested that hippocampal neurogenesis might be required for the effects of antidepressant treatments including antidepressant drugs and electroconvulsive therapy. The aim of this study was to examine chronic rTMS effects on hippocampal neurogenesis in rats.
Noise Estimation for Speech Enhancement in Non-Stationary Environments-A New Method

— This paper presents a new method for estimating the non-stationary noise power spectral density given a noisy signal. The method is based on averaging the noisy speech power spectrum using time and frequency dependent smoothing factors. These factors are adjusted based on signal-presence probability in individual frequency bins. Signal presence is determined by computing the ratio of the noisy speech power spectrum to its local minimum, which is updated continuously by averaging past values of the noisy speech power spectra with a look-ahead factor. This method adapts very quickly to highly non-stationary noise environments. The proposed method achieves significant improvements over a system that uses voice activity detector (VAD) in noise estimation.
Genetic variation of herpesvirus saimiri subgroup A transforming protein and its association with cellular src

Herpesvirus saimiri strain 11 of subgroup A contains a gene called the saimiri transformation-associated protein, STP, which is not required for viral replication but is required for in vitro immortalization and for the lymphoma-inducing capacity of the virus. To assess the effects of sequence variation on STP function, STP genes from six subgroup A isolates were cloned and sequenced. Sequence comparisons revealed extensive amino acid substitutions within the central region, but the acidic amino terminus and the hydrophobic carboxyl terminus were well conserved. Amino acid identities varied from 73 to 99% among all two-way comparisons. The highly conserved YAEV/I motif at amino acid residues 115 to 118 was preceded by negatively charged glutamic acid residues and thus matched very well the consensus sequence for binding to SH2 domains of src family kinases. The STPs of these subgroup A strains were shown to associate with cellular src and to be an in vitro substrate for src kinase. Mutational analysis of STP-A11 showed that binding to src kinase required the tyrosine residue at 115, showing that YAEV/I is a likely binding motif for src. Also, tyrosine phosphorylation of STP-A11 by src led to subsequent binding to lck and fyn in vitro. Thus, the association of STP with src is likely to be important for T-cell transformation by subgroup A strains of herpesvirus saimiri.
Protective effects of pomegranate peel against hematotoxicity, chromosomal aberrations, and genotoxicity induced by barium chloride in adult rats

Abstract Context Pomegranate peel (PP) has health benefits including antibacterial, antioxidant, anti-inflammatory, and antimutagenic properties. Objective This study investigated the biochemical composition and protective effects of PP against hematotoxicity and genotoxicity induced by barium chloride (BaCl2) in adult rats. Materials and methods Adult Wistar rats were divided into four groups of six each: control, barium (67 ppm via drinking water), PP (5% via diet), and their combination during 21 d. Oxidative stress was determined by MDA, AOPP, and antioxidant status: CAT, GPx, GSH, Vit C. Osmotic fragility (OF), chromosomal aberrations (CAs), and micronucleus (MN) assays were also studied. Results PP showed a rich composition of antioxidant compounds. DPPH test found IC50 value= 5.3 μg/mL and a high polysaccharides content (315 ± 5 mg/g of extract). In vivo study showed a decrease in red blood cells (70%) and platelet counts (46%), hemoglobin content (8%), hematocrit percent (7%), and an 80% increase of white blood cells in Ba-treated rats. A reduction in antioxidant status: catalase, glutathione peroxidase activities, glutathione, and vitamin C levels by 31, 21, 28, and 29%, respectively, and an increase in MDA (46%) and AOPP levels (72%) were also observed compared with controls. BaCl2-treatment showed a significant increase in the frequencies of total chromosomal aberrations with abnormal metaphases and micronucleus in bone-marrow cells. Oxidative stress induced by BaCl2 might be the major cause for chromosomal abnormalities leading to DNA damage. Discussion and conclusion A decrease in hematotoxic and genotoxic effects induced by PP is due to its powerful antioxidant capacity.
An association study of the Hermansky–Pudlak syndrome type 4 gene in schizophrenic patients

Objective We encountered two Japanese siblings who had Hermansky–Pudlak syndrome (HPS) and major mental disorders (schizophrenia and major depression) as well. As it is known that HPS is caused by a local mutation in one of the human genes, named HPS1 to HPS8 and PLDN (HPS9), encoding subunit proteins involved in endosomal trafficking pathways, here, we report the mutation causing the siblings disease and a case–control association study of schizophrenia using polymorphisms of a gene to be screened in the mutation analysis. Methods We analyzed three HPS-causing genes, HPS1, HPS4, and HPS7, to identify a genetic mutation involved in the siblings. A case–control association study of nine tagging single-nucleotide polymorphisms of the entire genetic region of the HPS4 gene resulting from the screening in the siblings was carried out for schizophrenic patients (n=422) and controls (n=578). Results The two patients with HPS were homozygous for nonsense mutation (T/T) for the c.541C>T (rs119471022) in the HPS4 gene, which is mapped to human chromosome 22q12.1. The same nonsense mutation existed in the heterozygous state (C/T) in their mother and in two other siblings. The genotypic distribution of rs9608491 (C/T) in intron 4 showed a trend toward an association with schizophrenia as indicated by a corrected P-value of 0.053 controlling for multiple testing. Haplotype analyses showed that two of two-locus haplotypes, and all of three-locus, four-locus, and five-locus haplotypes, as they share rs9608491, yielded significant evidence for association with schizophrenia as shown by the following omnibus P-values. When rs4822724, rs61276843, rs9608491, rs713998, and rs2014410, five haplotype tagging single-nucleotide polymorphisms, are assigned serial numerals (1, 2, 3, 4, and 5), the omnibus P-values for the resulting haplotypes were P=0.0039 for 2-3, P=0.0142 for 3-4, P=0.0083 for 1-2-3, P=0.0187 for 2-3-4, P=0.0191 for 3-4-5, P=0.0270 for 1-2-3-4, P=0.0246 for 2-3-4-5, and 0.0261 for 1-2-3-4-5. Conclusion These results suggest that the HPS4 gene confers a susceptibility to schizophrenia.
Exploring Diabetic Care Deficiencies and Adverse Events in Home Healthcare

&NA; Little information is available about the strength of the relationship between home healthcare practices and the potential adverse events the Centers for Medicare and Medicaid Services tracks through its uniform reporting system. We examined charts of patients who experienced a hyperglycemic or hypoglycemic emergent event to learn more about how home healthcare processes may contribute to an adverse event and to explore other factors that may contribute to a patient's health outcome. Implicit peer review, informed by an explicit review process, determined that 10% of the emergent care events were probably avoidable if home care had been optimal, 56% were potentially avoidable, and 34% were unavoidable.
Charging Unplugged: Will Distributed Laser Charging for Mobile Wireless Power Transfer Work?

Increasing the battery-recharge period of smartphones is becoming a challenge since their power consumption is increased as a result of enhanced functions that require sophisticated multimedia signal processing. An attractive solution is constituted by wireless charging, which is capable of replenishing the battery over the ether. Given this motivation, we present the fundamental physics and the related system structure of a promising wireless charging technique, i.e., distributed laser charging (DLC). Relying on DLC's unique features, we may be capable of transmitting approximately 2 W of power up to a distance of about 10 m. Following the comparison of the other three major wireless charging techniques, i.e., inductive coupling, magnetic resonance coupling, and microwave radiation, we demonstrate the benefits of DLC in the context of mobile applications. We then propose a pair of wireless charging network architectures, i.e., a DLC-aided, infrastructure-based network and a DLC-based ad-hoc network. These network architectures illustrate the potential of DLC in realizing the fully charged utopia for any device, anywhere, and anytime.
Comparing Data-Driven Learning Algorithms for PoS Tagging of Swedish

The aim of this study is a systematic evaluation and comparison of four state-of-the-art data-driven learning algorithms applied to part of speech tagging of Swedish. The algorithms included in this study are Hidden Markov Model, Maximum Entropy, Memory-Based Learning, and Transformation-Based Learning. The systems are evaluated from several aspects. Both the effects of tag set and the effects of the size of training data are examined. The accuracy is calculated as well as the error rate for known and unknown tokens. The results show differences between the approaches due to the different linguistic information built into the systems.
Interaction Among Apical Support, Levator Ani Impairment, and Anterior Vaginal Wall Prolapse

OBJECTIVE: To use a biomechanical model to explore how impairment of the pubovisceral portion of the levator ani muscle, the apical vaginal suspension complex, or both might interact to affect anterior vaginal wall prolapse severity. METHODS: A biomechanical model of the anterior vaginal wall and its support system was developed and implemented. The anterior vaginal wall and its main muscular and connective tissue support elements, namely the levator plate, pubovisceral muscle, and cardinal and uterosacral ligaments were included, and their geometry was based on midsagittal plane magnetic resonance scans. Material properties were based on published data. The change in the sagittal profile of the anterior vaginal wall during a maximal Valsalva was then predicted for different combinations of pubovisceral muscle and connective tissue impairment. RESULTS: Under raised intra-abdominal pressure, the magnitude of anterior vaginal wall prolapse was shown to be a combined function of both pubovisceral muscle and uterosacral and cardinal ligament (“apical supports”) impairment. Once a certain degree of pubovisceral impairment was reached, the genital hiatus opened and a prolapse developed. The larger the pubovisceral impairment, the larger the anterior wall prolapse became. A 90% impairment of apical support led to an increase in anterior wall prolapse from 0.3 cm to 1.9 cm (a 530% increase) at 60% pubovisceral muscle impairment, and from 0.7 cm to 2.4 cm (a 240% increase) at 80% pubovisceral muscle impairment. CONCLUSION: These results suggest that a prolapse can develop as a result of impairment of the muscular and apical supports of the anterior vaginal wall. LEVEL OF EVIDENCE: II-2
The Effect of Transplanted Bone Marrow Stem Cells on the Tongue of Irradiated Rats (Histological and Immunohistochemical study)

Normal tissue damage following radiotherapy (RT) is still a major problem in cancer treatment. So, the current work aimed at exploring the possible role of locally injected bone marrow derived mesenchymal stem cells (BM-MSCs) in ameliorating the side effects of ionizing radiation on the normal rat's tongue. Materials & Methods: Ten rats were used for isolating BM-MSCs, ten rats served as control group (G1) and twenty rats received a single radiation dose of 10 Gy to the head and neck region, then, they were equally divided into 2 experimental groups: Irradiated only group (G2) and Irradiated+MSCs group (G3). All animals were sacrificed at 2 weeks following irradiation. The tongue was examined histologically and immunohistochemically using anti-PCNA primary antibody. Results: Histological & immunohistochemical examination of the treated group (G3) revealed an obvious improvement in the histological structure of the tongue; compared to the irradiated group (G2); in addition to up regulated expression of PCNA, indicating improved cell proliferation rate. Conclusions: BM-MSCs have shown positive effect in protection against the side effects of radiotherapy on normal tissues, which was emphasized by their enhancing effect on the proliferative capacity of these tissues. (Aboushady, I.M.; Mubarak, R.T. El-mougy, S. A. F.; Rashed, L.A.; El-desouky, A.A. The Effect of Transplanted Bone Marrow Stem Cells on the Tongue of Irradiated Rats(Histological and Immunohistochemical study). J Am Sci 2012;8(11):553-561). (ISSN: 1545-1003). http://www.jofamericanscience. org. 84
Synthesis of plus strands of retroviral DNA in cells infected with avian sarcoma virus and mouse mammary tumor virus

The vast majority of plus strands synthesized in quail cells acutely infected with avian sarcoma virus were subgenomic in size, generally less than 3 kilobases (kb). A series of discrete species could be identified after agarose gel electrophoresis by annealing with various complementary DNAs, indicating specificity in the initiation and termination of plus strands. The first plus strand to appear (within 2 h postinfection) was similar in length to the long redundancy at the ends of linear DNA (0.35 kb), and it annealed with complementary DNAs specific for the 3' and 5' termini of viral RNA (Varmus et al., J. Mol. Biol. 120:50-82, 1978). Several subgenomic plus-strand fragments (0.94, 1.38, 2.3, and 3.4 kb) annealed with these reagents. At least the 0.94- and 1.38-kb strands were located at the same end of linear DNA as the 0.35-kb strand, indicating that multiple specific sites for initiation were employed to generate strands which overlapped on the structural map. We were unable to detect RNA liked to plus strands isolated as early as 2.5 h postinfection; thus, the primers must be short (fewer than 50 to 100 nucleotides), rapidly removed, or not composed of RNA. To determine whether multiple priming events are a general property of retroviral DNA synthesis in vivo, we also examined plus strands of mouse mammary tumor virus DNA in chronically infected rat cells after induction of RNA and subsequent DNA synthesis with dexamethasone. In this case, multiple, discrete subgenomic DNA plus strands were not found when the same methods applied to avian sarcoma virus DNA were used; instead, the plus strands present in the linear DNA of mouse mammary tumor virus fell mainly into two classes: (i) strands of ca. 1.3 kb which appeared early in synthesis and were similar in size and genetic content to the terminally repeated sequence in linear DNA; and (ii) plus strands of the same length as linear DNA. A heterogeneous population of other strands diminished with time, was not found in completed molecules, and was probably composed of strands undergoing elongation. These two retroviruses thus appear to differ with respect to both the number of priming sites used for the synthesis of plus strands and the abundance of full-length plus strands. On the other hand the major subgenomic plus strand of mouse mammary tumor virus DNA (1.3 kb) is probably the functional homolog of a major subgenomic plus strand of avian sarcoma virus DNA (0.35 kb). The significance of this plus strand species is discussed in the context of current models which hold that it is used as a template for the completion of the minus strand, thereby generating the long terminal redundancy.
Higher-order supersymmetric quantum mechanics

We review the higher‐order supersymmetric quantum mechanics (H‐SUSY QM), which involves differential intertwining operators of order greater than one. The iterations of first‐order SUSY transformations are used to derive in a simple way the higher‐order case. The second order technique is addressed directly, and through this approach unexpected possibilities for designing spectra are uncovered. The formalism is applied to the harmonic oscillator: the corresponding H‐SUSY partner Hamiltonians are ruled by polynomial Heisenberg algebras which allow a straight construction of the coherent states.
A Robust Low Cost Virtual Mouse Based on Face Tracking

This paper introduces a non-contact virtual mouse controlled by tracking the face movement. It is specially designed for the disabled with mobility impairments in the upper extremities. The whole work is based on the common web camera. Improved optical flow algorithm is proposed through locating the facial features defined by active appearance model. Experiments show it is robust to the various background and environment illumination. It also can effectively track the features when the face moves fast in a large scope.
Heavy-metal contamination and solid-phase fractionation in street dust

ABSTRACT Fourteen street-dust samples were collected from Hamedan, western Iran. Street-dust samples received different amounts of heavy-metal pollution. The samples were analyzed for total cadmium (Cd), copper (Cu), lead (Pb), nickel (Ni), and zinc (Zn), and binding forms of heavy metal were determined in five fractions. The results showed Cd was the only metal present appreciably, 25.21% and 25.92%, in the exchangeable and carbonates fractions, respectively, and Cu was the only metal predominantly associated, 31.77%, with organic fraction. Zn, 45.84%, was present mainly in the Fe–Mn oxide fraction, and the residual fraction was the most dominant solid phase pool of Ni and Pb, respectively, with 42.56% and 41.31%. The order of apparent mobility and potential metal bioavailability for these contaminated street-dust samples is Cd > Zn > Cu > Pb > Ni. The risk-assessment code results showed very high risk for Cd; medium risk for Cu, Pb, and Zn; and low risk for Ni.