Miracle-dz/UniFAR-FTUs huggingface dataset:
Pymanopt: A Python Toolbox for Optimization on Manifolds using Automatic Differentiation

Optimization on manifolds is a class of methods for optimization of an objective function, subject to constraints which are smooth, in the sense that the set of points which satisfy the constraints admits the structure of a differentiable manifold. While many optimization problems are of the described form, technicalities of differential geometry and the laborious calculation of derivatives pose a significant barrier for experimenting with these methods. We introduce Pymanopt (available at this https URL), a toolbox for optimization on manifolds, implemented in Python, that---similarly to the Manopt Matlab toolbox---implements several manifold geometries and optimization algorithms. Moreover, we lower the barriers to users further by using automated differentiation for calculating derivative information, saving users time and saving them from potential calculation and implementation errors.
Title The normative data and validity of the Chinese version of international outcome inventory for hearing aids (IOI-HA)

This study aimed at obtaining normative data and evaluating validity on the Chinese version of International Outcome Inventory for Hearing Aids (IOI-HA). The collected data would be useful to evaluate the effectiveness of hearing aid fitting in Hong Kong Cantonese population. IOI-HA was administered on 32 Cantonese-speaking hearing aid users. The Chinese version of IOI-HA showed high internal consistency. Factor analysis and inter-item correlations indicated the presence of two subscales, one of which could be regarded as benefit subscale and the other was residual problem subscale. Significant correlation were found between benefit and satisfaction scores on IOI-HA and satisfaction scores on the Profile of Hearing Aid Consumer Satisfaction (PHACS) for establishing convergent validity partially. Discriminant validity was found by having insignificant correlation of hearing aid use on IOI-HA and Chinese version of the Profile of Hearing Aid Performance (PHAP-C) as well as general satisfaction score on PHACS. The mean outcome scores collected did not differ substantially from those of other countries and they tended to be very positive in hearing aid fitting outcomes. Further investigation to include larger sample size with more diverse subject characteristics was recommended.
Use of Global and Acoustic Features Associated with Contextual Factors to Adapt Language Models for Spontaneous Speech Recognition

In this study, we propose a new method of adapting language models for speech recognition using para-linguistic and extralinguistic features in speech. When we talk with others, we often change the way of lexical choice and speaking style according to various contextual factors. This fact indicates that the performance of automatic speech recognition can be improved by taking the contextual factors into account, which can be estimated from speech acoustics. In this study, we attempt to find global and acoustic features that are associated with those contextual factors, then integrate those features into Recurrent Neural Network (RNN) language models for speech recognition. In experiments, using Japanese spontaneous speech corpora, we examine how i-vector and openSMILE are associated with contextual factors. Then, we use those features in the reranking process of RNN-based language models. Results show that perplexity is reduced by 16% relative and word error rate is reduced by 2.1% relative for highly emotional speech.
A causal relationship between sense of coherence and psycho-social work environment: from one-year follow-up data among Japanese young adult workers

The aim of this study was to use longitudinal data and investigate by sex the following four hypotheses on the relationship between sense of coherence (SOC) and work environment (WE): (i) a bidirectional cause-effect relationship exists; (ii) WE is the cause and SOC is the effect; (iii) SOC is the cause and WE is the effect; and (iv) no cause-effect relationship exists. Male and female subjects between the ages of 20 and 40 living in Japan were selected as subjects by two-stage stratified random sampling, and self-administered questionnaires were sent by mail between January and March 2007 (Time 1). A follow-up was conducted in the same way from January to March of 2008 (Time 2). Responses were obtained from 3,965 individuals (follow-up ratio: 82.6%). This study analyzed 1,291 males and 933 females who were at least 25 years old at Time 1 and who worked the same job in both time periods. The analysis was performed using a cross-lagged model under structural equation modeling. The second hypothesis was selected for both males and females based on the outcome of nested model comparisons. That is, a temporal cause-effect relationship was observed between SOC and WE for both males and females, with WE as the cause and SOC as the effect.
Anterior and posterior internal fixation of vertical shear fractures of the pelvis

A laboratory study was undertaken to evaluate the effectiveness of alternative methods of fixation of unilateral vertical shear fractures of the pelvis. Prior to experimental testing, a biomechanical analysis was performed to estimate the forces that displace the hemipelvis in the presence of two different patterns of injury: an interforaminal sacral fracture and a disruption of the sacroiliac joint. These lesions were then experimentally created in five unembalmed human pelvises and sequentially fixed with an external Hoffmann frame alone, a Hoffmann frame with sacral bars, or sacral bars with either one or two bone plates placed across the symphysis pubis. Each pelvis/fixator system was mechanically tested by loading along the direction of the resultant muscle force predicted by the biomechanical analysis. During loading the proximal migration of the ilium was continuously recored with a transducer. At intervals during loading, the three‐dimensional displacement of the detached hemipelvis at the pubic symphysis was also measured using a stereophotographic technique. With both the sacral frature and the sacroiliac disruption, the addition of posterior sacral rods substantially increased the strength and rigidity of fixation provided by the Hoffmann fixation frame alone (p < 0.01). In speciments with a sacral fracture, the use of anterior plates with posterior rods restored 65–71% of the strength of the intact pelvis, in comparison with 46% observed with the combination of sacral rods with an anterior Hoffmann frame (p < 0.01). All of the methods of fixation evaluated in this study were less successful in stabilizing the sacroiliac distruption. In this case there was no significant difference between the fixation achieved with one or two anterior bone plates or a Hoffmann frame placed anteriorly in combination with sacral rods placed posteriorly. In both patterns of injury treated with posterior sacral rods, the use of two anterior base plates led to no significant enhancement of the strength or the rigidity of fixation compared with one anterior plate alone.
Two vs. three or more primary recurrent pregnancy losses – are there any differences in epidemiologic characteristics and index pregnancy outcome?

Abstract Objective: To compare obstetric characteristics and pregnancy outcomes of patients following two vs. three or more primary recurrent pregnancy losses (RPL). Study design: A retrospective cohort study including 168 patients with primary RPL followed by subsequent (index) pregnancy, 124 patients with three or more consecutive RPL, and 60 patients with two consecutive RPL was performed. All patients were evaluated and treated in the RPL Clinic in the Soroka University Medical Center. Results: Obstetric characteristics of the study groups were similar. Women with three or more RPL compared to women with two RPL had a higher rate of abnormal thyroid stimulating hormone (TSH) levels (16.3 vs. 2.6%; P=0.033), higher rates of spontaneous pregnancy (91.7 vs. 77.4%; P<0.05), and higher rates of Clexane treatment (40.3% vs. 18.6%; P=0.016). In the index pregnancy, live birth rate was not statistically different between the two groups (81.1% in the two-RPL groups vs. 70.6% in the three-RPL group) nor was neonatal mortality. Conclusions: Patients with two RPL and three RPL had very similar obstetric characteristics and evaluation test results. Differences in index pregnancy outcomes were not statistically significant. Therefore, evaluation in primary RPL is recommended after two RPL.
Perturbations on domain walls and strings: A covariant theory.

A covariant formalism is developed for describing perturbations on vacuum domain walls and strings. The treatment applies to arbitrary domain walls in ({ital N}+1)-dimensional flat spacetime, including the case of bubbles of a true vacuum nucleating in a false vacuum. Straight strings and planar walls in de Sitter space, as well as closed strings and walls nucleating during inflation, are also considered. Perturbations are represented by a scalar field defined on the unperturbed wall or string world sheet. In a number of interesting cases, this field has a tachyonic mass and a nonminimal coupling to the world-sheet curvature.
Irreversible Inhibition of Human Immunodeficiency Virus Type 1 Integrase by Dicaffeoylquinic Acids

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) and other retroviruses require integration of a double-stranded DNA copy of the RNA genome into the host cell chromosome for productive infection. The viral enzyme, integrase, catalyzes the integration of retroviral DNA and represents an attractive target for developing antiretroviral agents. We identified several derivatives of dicaffeoylquinic acids (DCQAs) that inhibit HIV-1 replication in tissue culture and catalytic activities of HIV-1 integrase in vitro. The specific step at which DCQAs inhibit the integration in vitro and the mechanism of inhibition were examined in the present study. Titration experiments with different concentrations of HIV-1 integrase or DNA substrate found that the effect of DCQAs was exerted on the enzyme and not the DNA. In addition to HIV-1, DCQAs also inhibited the in vitro activities of MLV integrase and truncated variants of feline immunodeficiency virus integrase, suggesting that these compounds interacted with the central core domain of integrase. The inhibition on retroviral integrases was relatively specific, and DCQAs had no effect on several other DNA-modifying enzymes and phosphoryltransferases. Kinetic analysis and dialysis experiments showed that the inhibition of integrase by DCQAs was irreversible. The inhibition did not require the presence of a divalent cation and was unaffected by preassembling integrase onto viral DNA. The results suggest that the irreversible inhibition by DCQAs on integrase is directed toward conserved amino acid residues in the central core domain during catalysis.
Assessing clinical correlates of self-rated disability in patients with multiple sclerosis

Background Multiple sclerosis (MS) is associated with significant impairment. Objective The objective of this article is to identify and compare clinical measures that can predict self-rated disability in patients with MS using the World Health Organization Disability Assessment Schedule II (WHODAS-II). Methods Patients with MS and healthy controls were consecutively recruited at one center. Patients were evaluated for cognitive function assessment, neurological status, perceived disability, mood, fatigue and disease duration. Controls underwent neuropsychological evaluation only. Data were analyzed using multivariate regression. Results WHODAS-II total score was predicted by fatigue (p < 0.001) and neurological status (p < 0.05). Student’s t test comparisons between published WHODAS-II normative data and the enrolled cohort of patients with MS showed significantly worse (p < 0.05) scores for patients on mobility, self-care, life activities, participation and total score domains, but not in cognition. Group differences between patients with MS (n = 61) and controls (n = 61) were significant in all cognitive measures except one verbal memory test subscale. Memory function correlated best with the social participation domain of the WHODAS-II. Conclusions Self-reported disability in patients with MS was most strongly influenced by fatigue and to a lesser extent by physical disability. Although cognitive function does affect self-assessment of disability, this is not captured by patients on the WHODAS-II cognitive domain.
The Meaning of Relocation among Elderly Religious Sisters

The meaning of involuntary, intra-institutional relocation (a move in primary living space) was constructed in this qualitative study through semistructured interviews with 12 elderly religious sisters. A thematic analysis of the data elicited from audiotape-recorded interviews was conducted. Overall, themes emerging from the sisters'discussion of the relocation included relocation as preparation for the future (to ensure their care in advancing years) and possibilities and consequences (resulting in improved living conditions together with sacrifice, uprooting, isolation, and distancing). Although relocation was seen as a largely positive event, it also had negative meaning for the subjects.
Dose-related effects of Quercetin in the human breast carcinoma MCF-7 cell line

Quercetin is a flavonol present at high levels in onions, apples, tea and red wine. Although quercetin has been epidemiologically associated with bioactive protective effects, this compound has also been shown to be mutagenic and toxic in short-term in vitro test systems. This study evaluated quercetin for toxicity in the MCF-7 cell line in the presence or absence of benzo[a]pyrene (B[a]P), a known DNA-reactive carcinogen. In the clonogenic assay, 2.5 × 10 2
Rad 17 recruits the MRE 11-RAD 50-NBS 1 complex to regulate the cellular response to DNA double-strand breaks

The MRE11-RAD50-NBS1 (MRN) complex is essential for the detection of DNA double-strand breaks (DSBs) and initiation of DNA damage signaling. Here, we show that Rad17, a replication checkpoint protein, is required for the early recruitment of the MRN complex to the DSB site that is independent of MDC1 and contributes to ATM activation. Mechanistically, Rad17 is phosphorylated by ATM at a novel Thr622 site resulting in a direct interaction of Rad17 with NBS1, facilitating recruitment of the MRN complex and ATM to the DSB, thereby enhancing ATM signaling. Repetition of these events creates a positive feedback for Rad17-dependent activation of MRN/ATM signaling which appears to be a requisite for the activation of MDC1-dependent MRN complex recruitment. A point mutation of the Thr622 residue of Rad17 leads to a significant reduction in MRN/ATM signaling and homologous recombination repair, suggesting that Thr622 phosphorylation is important for regulation of the MRN/ATM signaling by Rad17. These findings suggest that Rad17 plays a critical role in the cellular response to DNA damage via regulation of the MRN/ATM pathway.
Structural basis for the Nanos-mediated recruitment of the CCR4–NOT complex and translational repression

Nanos family RNA-binding proteins play essential roles in metazoan germ cell fate and survival, yet the underlying mechanism has not been elucidated. Bhandari et al. now provide the structural basis for CCR4–NOT complex recruitment by vertebrate Nanos. The authors show that three human Nanos paralogs interact with the CNOT1 C-terminal domain through a short, conserved CNOT1-interacting motif (NIM). This work indicates that NIMs are the major determinants of the translational repression mediated by Nanos and identifies the CCR4–NOT complex as the main effector for Nanos function.
Increased Expression of Intracisternal A-Particle RNA in Regenerated Myeloid Cells after X Irradiation in C3H/He Inbred Mice

Abstract Ishihara, H. , Tanaka, I. , Furuse, M. and Tsuneoka, K. Increased Expression of Intracisternal A-Particle RNA in Regenerated Myeloid Cells after X Irradiation in C3H/He Inbred Mice. Myeloid leukemia cells were derived from regenerated hematopoietic cells damaged by sublethal doses of X radiation in C3H/He inbred mice. We previously found that within the genome of the myeloid leukemia cells, a retrotransposon, the intracisternal A-particle (IAP) element, is integrated. Levels of IAP RNA, the source of cDNA for the integration, were analyzed quantitatively in C3H mice. Higher levels of IAP transcripts were observed in normal cells, particularly in hematopoietic cells, from C3H/He mice, than in those from C57BL/6J and STS/A mice. In the C3H/He mice, an approximately twofold increase in IAP RNA was found in the regenerated spleen and bone marrow cells at 5 days and from 12 to 90 days after whole-body X irradiation. In addition, an increased level of IAP RNA was observed in all the myeloid leukemia cells derived from C3H/He mice. This suggests that the elevated levels of IAP RNA in the regenerated hematopoietic cells after irradiation contribute to the increase in retrotransposition of IAP found in myeloid leukemia cells from C3H/He mice.
Characterization of membrane-associated Pseudomonas aeruginosa Ras-like protein Pra, a GTP-binding protein that forms complexes with truncated nucleoside diphosphate kinase and pyruvate kinase to modulate GTP synthesis

We report the purification and characterization of a protein from the membrane fraction of Pseudomonas aeruginosa showing intrinsic guanosine triphosphatase (GTPase) activity. The protein was purified as a 48-kDa polypeptide capable of binding and hydrolyzing GTP. The N-terminal sequence of the purified protein revealed its similarity to the Escherichia coli Ras-like protein (Era), and the protein cross-reacted with anti-Era antibodies. This protein was named Pseudomonas Ras-like protein (Pra). Anti-Pra antibodies also cross-reacted with E. coli Era protein. Pra is autophosphorylated in vitro, with phosphotransfer of the terminal phosphate from [gamma-32P]GTP but not [gamma-32P]ATP. Pra is capable of complex formation with the truncated 12-kDa form of nucleoside diphosphate kinase (Ndk) but not with the 16-kDa form. Purified Pra was also shown to physically interact with pyruvate kinase (Pk); Pk and Pra can form a complex, but when the 12-kDa Ndk, Pk, and Pra are all present, Pk has a higher affinity than Pra for forming a complex with the 12-kDa Ndk. The 12-kDa Ndk-Pra complex catalyzed increased synthesis of GTP and dGTP and diminished synthesis of CTP and UTP or dCTP and dTTP relative to their synthesis by uncomplexed Ndk. Moreover, the complex of Pra with Pk resulted in the specific synthesis of GTP as well when Pra was present in concentrations in excess of that of Pk. Membrane fractions from cells harvested in the mid-log phase demonstrated very little nucleoside triphosphate (NTP)-synthesizing activity and no detectable Ndk. Membranes from cells harvested at late exponential phase showed NTP-synthesizing activity and the physical presence of Ndk but not of Pk or Pra. In contrast, membrane fractions of cells harvested at early to late stationary phase showed predominant GTP synthesis and the presence of increasing amounts of Pk and Pra. It is likely that the association of Pra with Ndk and/or Pk restricts its intrinsic GTPase activity, which may modulate stationary-phase gene expression and the survival of P. aeruginosa by modulating the level of GTP.
The P2Y2 Nucleotide Receptor Mediates UTP-induced Vascular Cell Adhesion Molecule-1 Expression in Coronary Artery Endothelial Cells*

P2Y2 receptor up-regulation and activation induces intimal hyperplasia and monocyte/macrophage infiltration in the collared rabbit carotid artery model of vascular injury, suggesting a potential role for P2Y2 receptors in monocyte recruitment by vascular endothelium. In this study, we addressed the hypothesis that activation of P2Y2 receptors by extracellular nucleotides modulates the expression of adhesion molecules on vascular endothelial cells that are important for monocyte recruitment. Results indicated that the equipotent P2Y2 receptor agonists UTP or ATP (1–100 μm) stimulated the expression of vascular cell adhesion molecule-1 (VCAM-1) in human coronary artery endothelial cells (HCAEC) in a time- and dose-dependent manner. P2Y2 antisense oligonucleotides inhibited VCAM-1 expression induced by UTP but not by tumor necrosis factor-α. Furthermore, UTP induced VCAM-1 expression in human 1321N1 astrocytoma cell transfectants expressing the recombinant P2Y2 receptor, whereas vector-transfected control cells did not respond to UTP. The effect of UTP on VCAM-1 expression in HCAEC was prevented by depletion of intracellular calcium stores with thapsigargin or by inhibition of p38 mitogen-activated protein kinase or Rho kinase, but was not affected by inhibitors of the mitogen-activated protein/extracellular signal-regulated kinase pathway (i.e. MEK1/2). Consistent with a role for VCAM-1 in the recruitment of monocytes, UTP or ATP increased the adherence of monocytic U937 cells to HCAEC, an effect that was inhibited by anti-VCAM-1 antibodies. These findings suggest a novel role for the P2Y2 receptor in the p38- and Rho kinase-dependent expression of VCAM-1 that mediates the recruitment of monocytes by vascular endothelium associated with the development of atherosclerosis.
An MLD scheme for interference suppression based on noise subspace projection for MIMO-OSTBCs system

This paper presents an interference suppression reception scheme for the multiple input multiple output (MIMO) communication systems using orthogonal space-time block codes (OSTBCs) in strong interference scenario. Based on the noise subspace projection, the maximum likelihood decoding (MLD) for OSTBCs can be achieved by simple linear processing in this scheme. Moreover, the approach to obtain the efficient channel state information (CSI) in strong interference scenario is also included in this proposed scheme. The simulation results are given to verify the interference suppression ability of the proposed scheme. Compared with other suppression scheme, the proposed scheme has better SER performance and is more flexible in practical applications.
Diagnosis of alveolar rhabdomyosarcoma in effusion cytology: a diagnostic pitfall

Rhabdomyosarcoma (RMS) is a rare malignancy in adults, accounting for less than 5% of soft tissue sarcomas in this age group. Sarcomas account for approximately 5% of malignant effusions. Expression of neuroendocrine and epithelial markers by alveolar RMS has been demonstrated recently, highlighting a diagnostic pitfall in effusion cytology, especially when dealing with small, round cell tumours (SRCT).