Miracle-dz/UniFAR-FTUs huggingface dataset:
Parameter tuning and evaluation of an affinity prediction using protein-protein docking

We have developed a system, which we call affinity evaluation and prediction (AEP) system, to evaluate and predict the partners in protein-protein interaction (PPI) by using a statistical method for calculated docking scores. The complex-protein structures obtained in shape complementary evaluation are selected by a newly developed clustering method called grouping. Our previous experiments showed that the AEP system has a tendency to give different accuracy depending on biologically significant protein dataset and data scale (20×20= 400 protein pairs). In this study, we set a data scale (54×54=2916 protein pairs) including 54 biologically significant complexes. As a result of receiver operating characteristics (ROC) analysis, the AEP system obtained 55.6% sensitivity (=recall), 70.6% specificity, 3.44% precision, 70.3% accuracy, 6.48% F-measure and an area under the curve (AUC) of 0.655. The prediction accuracy of F-measure was about 1.82 times higher than that of a random sampling (F-measurerandom=3.57%). By optimizing the grouping procedure, the AEP system successfully predicted 30 protein pairs (among 54 pairs) that were biologically significant.
Physical Educators' Perceptions of Their Use of NASPE Standards.

The rate of childhood obesity in the United States is approximately 17%. Because physical education can be a key intervention strategy against this epidemic, this study was conducted to determine physical educators’ perceptions on their use of recommended national standards specifically focused on physical fitness and activity in their classroom. An online survey was distributed to 101 physical education teachers from nine states in which participants were asked to provide their opinion of several Likert-based questions that ascertained use of National Association for Sport and Physical Education (NASPE) Standards 1, 3, and 4. Teachers were found to incorporate the components of these standards at varying rates. More experienced physical education teachers spent less instructional time on movement fundamentals and combining skills than did less experienced teachers. Furthermore, they assessed student enjoyment significantly less in higher grades than in lower grades. Physical educators teaching higher grade levels as well as those with more contact time with students spent less instructional time teaching movement fundamentals, balancing skills, carrying and lifting techniques, and motor skills. Over 40% of participants had 2 or less hours of contact time per week. Thus, how effective a physical educator can be with limited time is uncertain, and although physical educators have a unique opportunity to address childhood obesity challenges, they must be provided the time and opportunity to do so.
Data validation in the presence of imprecisely known correlations

This paper derives fundamental results for data validation in the presence of imprecisely known correlations. Given a constraint on the maximum absolute correlation of a given estimate and measurement data, a tight upper bound for the joint covariance matrix is derived, which finally yields a modified Mahalanobis distance. The special cases of one-dimensional and two-dimensional random variables are discussed.
Navy's CFC & Halon Elimination Program

The domestic production of the most powerful Ozone-Depleting Substances (ODSs) has permanently ceased and the abundant supplies of a number of inexpensive refrigerants, fire-fighting agents, and solvents, once taken for granted, are now a thing of the past The Navy's original strategy of conserving ODSs, converting systems and processes where feasible, relying on strategic reserves where necessary, and developing “ozone-friendly” equipment for new-design surface ships and submarines is succeeding. The purpose of this paper is to document the Navy's efforts to date relative to combating the threat to uninterrupted Fleet operations posed by the cessation of ODS production. Specifically, this paper addresses the Navy's shipboard conversion programs for air-conditioning and refrigeration (AC&R) systems, the development of next-generation AC&R systems, the selection of halon substitutes for new-construction fire-fighting systems, and the Navy's alternative to CFC-113 in the cleaning of critical oxygen systems.
Response to Sugiharto, "Comprehensible input as social alignment."

It is true that my work and the work of my associates has focused mainly on the cognitive aspects of language aquisition. But it is not true that we have ignored non-cognitive variables. Our papers have discussed the role of poverty, the importance of access to reading material, the role of librarians, the role of parents, the function of interaction, club membership, personality, technology, etc.
Hitting time for doubly-weighted graphs with application to robotic surveillance

This article provides analysis results for the weighted hitting time and the pairwise weighted hitting time of a Markov chain. This concepts are useful in many applications from robotics to patrolling, environment monitoring and resources optimization. The aforementioned quantities are a performance indexes which measure the expected time taken by a random walker to travel from an arbitrary node of a graph to a second randomly selected node and the expected time to travel between two chosen nodes. These metrics can be used as objective function in optimization problems. In fact we propose a numerical example applied to robotic surveillance where the weighted hitting time is our cost to minimize with respect to the transition matrix of the agent.
Differentiation of human umbilical cord-derived mesenchymal stem cells into hepatocytes in vitro.

OBJECTIVE The stem cell based therapy is a potential alternative to liver transplantation. The aim of the study is to investigate the hepatocytic differentiation ability of human umbilical cord derived mesenchymal stem cells (HUC-MSCs) in vitro. METHODS The HUC-MSCs were isolated from Wharton's jelly of human umbilical cord. The cells were identified by assessing the stem cell markers. The HUC-MSCs were characterized by multipotency of differentiation. We modified the hepatogenic differentiation protocol and examine the function of differentiated cell by Periodic acid-Schiff (PAS) staining and Low-Density Lipoprotein (LDL) uptake. The protein expressions of Total protein (TP), Albumin (ALB), Globulin (GLB), Urea (BUN) and α-fetoprotein (AFP) were also detected. RESULTS The cells of the hepatogenic differentiation group showed the function of hepatocyte. Protein expressions of TP, ALB, GLB BUN and AFP improve that the HUC-MSCs are able to different into the functional hepatogenic-like cell. CONCLUSION The above founding indicated that the HUC-MSCs are able to different into the functional hepatogenic-like cell by present method.
Asymptotic Study on the Extendability of Equilibria of Nematic Polymers

This paper addresses the extendability of equilibrium solutions of pure nematic liquid crystal polymers. More precisely, we apply the asymptotic analysis to show that the Jacobian of the nonlinear system is nonzero for both the prolate branch and the oblate branch when the nematic strength is large enough. This result implies the existence and uniqueness of the equilibrium solutions in the presence of small perturbations.
Detection of stress/anxiety state from EEG features during video watching

This paper studies the effect of stress/anxiety states on EEG signals during video sessions. The levels of arousal and valence that are induced to each subject while watching each video are self rated. These levels are mapped in stress and relaxed states and subjects that fufill criteria of adequate anxiety/stress scale were chosen leading to a subset of 18 subjects. Then, temporal, spectral and non linear EEG features are evaluated for being able to represent accurately states under investigation. Feature selection schemes choose the most significant of them in order to provide increased discrimination ability between relaxed and anxiety/stress states.
Latent Tuberculosis Infection among Immigrant and Refugee Children Aged 2-14 Years Who Arrived in the United States in 2008-2012

Background: According to Centers for Disease Control and Prevention (CDC) tuberculosis (TB) report TB case rate dropped from 3.2 to 3.0 per 100,000 person in 2013 in the U.S, which was a 4.3% decrease from 2012, but the proportion of total cases occurring in foreign-born persons reached to 65% of the national case total. This proportion has been increasing since 1993. Studies found that progression of latent tuberculosis infection (LTBI) to active TB (reactivation TB) contributed a large proportion to TB cases among foreign-born persons and posed a huge challenge to TB elimination in the U.S. The Division of Global Migration and Quarantine (DGMQ) in CDC provides Tuberculosis Screening and Treatment Technical Instructions (TB TI) for U.S.-bound immigrant and refugee overseas medical screening. The 2007 TB TI made several changes to enhance overseas medical screening for TB. One of them is requiring applicants aged 2-14 years who live in countries with a World Health Organization (WHO)-estimated TB incidence rate equal or higher than 20 cases per 100,000 population to have a tuberculin skin test (TST) or interferon gamma release assay (IGRA) to detect TB/LTBI. Objectives: To assess LTBI prevalence among immigrant and refugee children aged 2-14 years who arrived in the United States in 2008-2012 and to explore demographic and geographic predictors among LTBI cases. Methods: Using DGMQ data from 2008-2012, LTBI prevalence was calculated. Regression analyses were used to examine predictors of LTBI risk based upon geographic and select demographic characteristics (country of origin, sex, country-specific LTBI prevalence rate). Results: LTBI prevalence of all 199 immigrant and refugee arrival countries vs top 16 arrival countries were 6.30% and 8.76%, respectively. Top 16 arrival countries contributed to 68.40% arrivals but contributed to 95.08% of LTBI cases. LTBI prevalence of both populations showed an increasing trend in 2008-2012. The highest five prevalence countries were the Philippines (42.74%) Vietnam (9.35%), Mexico (8.71%), Bhutan (8.31%) and China (7.80%). Regression coefficient estimates (i.e., log odds) for country of origin predictor were significant (p<.0001) (all tests α = 0.05) for 14 out of 16 top arrival countries. Coefficient estimates for the predictors of female percentage, 2007 TB TI percentage, WHO TB prevalence, female less than 50 percent and its interaction with female percentage were all significant (p<.0001). Conclusions: Diagnosing and treating LTBI and continuing the battle against TB globally are critical to TB elimination in the U.S. 2007 TB TI has contributed to detecting LTBI cases, should be implemented vigorously in immigrant and refugee overseas medical screening. Receiving states should address their follow-up gaps to ensure the completion of TB/LTBI treatment. Resources need to be allocated properly to states with high TB/LTBI burden.
Multinational Spillovers through Worker Turnover ∗

Labor turnover is a commonly-cited mechanism for the transmission of spillovers from multinational to domestic firms, but until now there has been little direct evidence for this mechanism. Using a novel matched establishment-worker database from Brazil, I present evidence consistent with the existence of positive multinational spillovers through worker mobility in Brazil. The paper explores where spillovers occur and how they are absorbed. The main results suggest that the magnitude of wage spillovers from multinational establishments depends on the sector and the worker under consideration. The results provide support for the hypothesis that higher-skilled former multinational-establishment workers are better able to convey information and higher-skilled incumbent domestic-establishment workers are better able to absorb information. Information is best transferred between similarly skilled groups of highskilled workers and from higher-skilled former multinational-establishment workers to lower-skilled incumbent domestic-establishment workers. The results are robust to various model specifications, including worker and establishment fixed effects. ∗I am grateful to Marc Muendler and Jim Rauch for their guidance and support throughout this research, and to Eli Berman, Julie Cullen, Gordon Hanson, Craig McIntosh, and Giovanni Peri for helpful discussions. I also thank seminar participants at the UCSD Department of Economics, Applied Lunch Seminar, the UCSD joint Department of Economics—Graduate Institute of International Relations and Pacific Studies, International and Development Seminar, and the Santa Cruz Center for International Economics (SCCIE) 10th Annual Conference. Special thanks to Paulo Furtado de Castro for help with the RAIS data, and to Patricia Vanderlei Fernandes and Paulo Marcelo Cavalcanti Muniz of the Brazilian Central Bank for providing the RDE-IED data. Financial support from the Institute for International, Comparative, and Area Studies, the Dean of Social Sciences, and the Center for Iberian and Latin American Studies at the University of California, San Diego is acknowledged. †Department of Economics, University of California, Santa Cruz, 437 Engineering 2, Santa Cruz, CA 95064, jpoole@ucsc.edu, (831) 459-5397.
Canine T-cell Lymphomas: A Morphological, Immunological, and Clinical Study of 46 New Cases

The aim of this study is to report 46 new cases of canine T-cell lymphomas among a series of 140 lymphomas studied by immunophenotyping (incidence 32.8%). According to the updated Kiel classification adapted to the canine species, 13 were classified as low-grade and 33 as high-grade lymphomas. Among the low-grade lymphomas, five were small clear-cell lymphomas, three were pleomorphic small-cell lymphomas, and five mycosis fungoides. Among the high-grade cases, there were 11 pleomorphic mixed-, small-, and largecell lymphomas, 6 pleomorphic large-cell lymphomas, 11 lymphoblastic lymphomas, and 5 unclassifiable highgrade plasmacytoid lymphomas. The cytohistologic features were highly suggestive of a T-cell phenotype on the basis of cell morphology (irregular nuclei and clear cytoplasms) (30/46 cases), a T-cell zone pattern, and the presence of hyperplastic postcapillary venules (22/46 cases). All 46 cases were CD3+ CD79a-, and among 34 cases investigated for CD4 and CD8 expression, 13 were CD4+CD8-, 13 were CD8+CD4-, and 8 were CD4CD8 double positive or double negative. The pleomorphic mixed lymphomas were mainly CD4+CD8- (6/7) and the lymphoblastic lymphomas were double positive or double negative (6/8). The main clinical, hematologic, and biochemical features were generalized (28/46) or regional lymphadenopathy (16/46), hepatosplenomegaly (15/46), extranodal involvement (11/46), mediastinal mass (9/46), and leukemia (8/46), which were mainly present in cases of lymphoblastic lymphomas and hypercalcemia (16/46).
Conflict resolution for pipelined layered LDPC decoders

Many of the current LDPC implementations of DVB-S2, T2 or WiMAX standard use the so-called layered architecture combined with pipeline. However, the pipeline process may introduce memory access conflicts. The resolution of these conflicts requires careful scheduling combined with dedicated hardware and/or idle cycle insertion. In this paper, based on the DVB-T2 example, we explain explicitly how the scheduling can solve most of the pipeline conflicts. The two contributions of the paper are 1) how to split the matrix to relax the pipeline conflicts at a cost of a reduced maximum available parallelism 2) how to project the problem of the research of an efficient scheduling to the well-known “Travelling Salesman Problem” and use a genetic algorithm to solve it.
Gesture-based visualization interaction design in handheld devices

A new gesture-based visualization interaction design process model was proposed to support the method of gesture-based visualization interaction design in handheld devices. The development of handheld device, especially smart phones, user-centered interaction design theory and the circumstance of the application of gestures in handheld devices were studied. The example of And-Enjoy, which is an app based on android system, was shown to verify the effectiveness and practicality of the model through design evaluation.
The Impact of Opioids on the Endocrine System

ObjectivesOpioids have been used for medicinal and analgesic purposes for centuries. However, their negative effects on the endocrine system, which have been known for some times, are barely discussed in modern medicine. Therefore, we conducted a systematic review of the impact of opioids on the endocrine system. MethodsA review of the English language literature on preclinical and clinical studies of any type on the influence of opioids on the endocrine system was conducted. Preliminary recommendations for monitoring and managing these problems were provided. ResultsLong-term opioid therapy for either addiction or chronic pain often induces hypogonadism owing to central suppression of hypothalamic secretion of gonadotropin-releasing hormone. Symptoms of opioid-induced hypogonadism include loss of libido, infertility, fatigue, depression, anxiety, loss of muscle strength and mass, osteoporosis, and compression fractures in both men and women; impotence in men; and menstrual irregularities and galactorrhea in women. In view of the increased use of opioids for chronic pain, it has become increasingly important to monitor patients taking opioids and manage endocrine complications. Therefore, patients on opioid therapy should be routinely screened for such symptoms and for laboratory abnormalities in sex hormones. ConclusionsOpioid-induced hypogonadism seems to be a common complication of therapeutic or illicit opioid use. Patients on long-term opioid therapy should be prospectively monitored, and in cases of opioid-induced hypogonadism, we recommend nonopioid pain management, opioid rotation, or sex hormone supplementation after careful consideration of the risks and benefits.
Serial dependence in face attractiveness judgements tolerates rotations around the yaw axis but not the roll axis

ABSTRACT Once a face is detected, its retinal image will be continually distorted by changes in eye position, noise, lighting and many other factors. Yet from one moment to the next our perception of a face is stable. Recent advances have indicated there is a mechanism for achieving the continuous perception of a person’s identity that pools across prior and present visual inputs. There is still debate as to whether the perception of face attractiveness is also serially dependent. Here we investigate continuity in the perception of attractiveness using a one back [t−1] effect as a marker of serial dependence. Our results show that face attractiveness is biased towards the attractiveness of the previous face, and that this effect is robust despite changes in viewpoint involving rotations around the yaw axis. However, face attractiveness perception is released from this form of rapid adaption when the previously seen face differed in orientation due to a rotation around the roll axis.
Effects of Visual Concept-based Post-retrieval Clustering in ImageCLEFphoto 2008

We examined the effectiveness of post-retrieval clustering that was based on the visual similarities among images to enhance the instance recall in the photo retrieval task of ImageCLEF 2008. The visual similarities are defined by the example visual concepts that were provided for the automatic photo indexing task. We tested two types of visual concepts and two kinds of clustering methods, hierarchical and modified k-means clustering. In all the runs, we used only the title fields in the search topics; we used either only the title fields or both the title and description fields of the annotations in English. The experimental results showed that hierarchical clustering can enhance instance recall while preserving the precision when certain parameters are appropriately set.
DEVELOPMENT AND DISEASE Loss of Emx 2 function leads to ectopic expression of Wnt 1 in the developing telencephalon and cortical dysplasia

During development of the elegantly structured mammalian cerebral cortex, generation and subsequent migration of specialized neurons and glia within the brain follows a characteristic sequence. The earliest differentiated neurons emigrate from the telencephalic ventricular zone to form a superficial primordial layer called the preplate (Allendoerfer and Shatz, 1994). In mice, the marginal zone (MZ, layer I) and subplate (SP) derive from splitting of the preplate at ~11-12.5 days postcoitum (dpc) as successive waves of neurons from the underlying ventricular zone undergo radial migration into the cortical plate proper (layers II-VI). The MZ and SP comprise a heterogeneous population of cells with neuronal properties, including reelin-expressing Cajal-Retzius (CR) cells, subpial granule cells (glutamate-positive) and subpallial-derived interneurons (GABA-positive) (Fairen et al., 2002; Meyer et al., 1998; Parnavelas, 2000; Zecevic et al., 1999). Important roles for MZ and SP cells during tangential and radial migration of cortical neurons have been previously described (Parnavelas, 2000; Xie et al., 2002). For example, proper formation of the MZ and SP has been shown to be necessary for tangential emigration of GABA-expressing interneurons from ventral forebrain regions (e.g. the ganglionic eminence) into the cortical plate (Lavdas et al., 1999). Second, cells in the MZ provide repulsive or stop cues to radially migrating cortical 2275 Development 130, 2275-2287 © 2003 The Company of Biologists Ltd doi:10.1242/dev.00421
Antischistosomal Activity of Trioxaquines: In Vivo Efficacy and Mechanism of Action on Schistosoma mansoni

Schistosomiasis is among the most neglected tropical diseases, since its mode of spreading tends to limit the contamination to people who are in contact with contaminated waters in endemic countries. Here we report the in vitro and in vivo anti-schistosomal activities of trioxaquines. These hybrid molecules are highly active on the larval forms of the worms and exhibit different modes of action, not only the alkylation of heme. The synergy observed with praziquantel on infected mice is in favor of the development of these trioxaquines as potential anti-schistosomal agents.