Miracle-dz/UniFAR-FTUs huggingface dataset:
Test MM-PB/SA on True Conformational Ensembles of Protein-Ligand Complexes

The molecular mechanics Poisson-Boltzmann surface area (MM-PB/SA) method has been popular for computing protein-ligand binding free energies in recent years. All previous evaluations of the MM-PB/SA method are based upon computer-generated conformational ensembles, which may be affected by the defective computational methods used for preparing these conformational ensembles. In an attempt to reach more convincing conclusions, we have evaluated the MM-PB/SA method on a set of 24 diverse protein-ligand complexes, each of which has a set of conformations derived from NMR spectroscopy. Our results indicate that both MM-PB/SA and molecular mechanics generalized Born surface area (MM-GB/SA) are able to produce a modest correlation between their results and the experimentally measured binding free energies on our test set. In particular, both MM-PB/SA and MM-GB/SA produced better results by using a representative structure (R = 0.72-0.79) rather than averaging over the conformational ensemble of each given complex (R = 0.61-0.74). A head-to-head comparison with four selected scoring functions (X-Score, PLP, ChemScore, and DrugScore) on the same test set reveals that MM-PB/SA and MM-GB/SA results are marginally better than those produced by scoring funcitons, supporting the value of the MM-PB/SA method. Nevertheless, scoring functions are still more cost-effective options, especially for high-throughput tasks.
Collaborative Filtering beyond the User-Item Matrix

Over the past two decades, a large amount of research effort has been devoted to developing algorithms that generate recommendations. The resulting research progress has established the importance of the user-item (U-I) matrix, which encodes the individual preferences of users for items in a collection, for recommender systems. The U-I matrix provides the basis for collaborative filtering (CF) techniques, the dominant framework for recommender systems. Currently, new recommendation scenarios are emerging that offer promising new information that goes beyond the U-I matrix. This information can be divided into two categories related to its source: rich side information concerning users and items, and interaction information associated with the interplay of users and items. In this survey, we summarize and analyze recommendation scenarios involving information sources and the CF algorithms that have been recently developed to address them. We provide a comprehensive introduction to a large body of research, more than 200 key references, with the aim of supporting the further development of recommender systems exploiting information beyond the U-I matrix. On the basis of this material, we identify and discuss what we see as the central challenges lying ahead for recommender system technology, both in terms of extensions of existing techniques as well as of the integration of techniques and technologies drawn from other research areas.
Alpha‐lipoic acid decreases hepatic lipogenesis through adenosine monophosphate‐activated protein kinase (AMPK)‐dependent and AMPK‐independent pathways

Fatty liver is common in obese subjects with insulin resistance. Hepatic expression of sterol regulatory element binding protein‐1c (SREBP‐1c), which plays a major role in hepatic steatosis, is regulated by multiple factors, including insulin, adenosine monophosphate–activated protein kinase (AMPK), liver X receptors (LXRs), and specificity protein 1. Alpha‐lipoic acid (ALA), a naturally occurring antioxidant, has been shown to decrease lipid accumulation in skeletal muscle by activating AMPK. Here we show that ALA decreases hepatic steatosis and SREBP‐1c expression in rats on a high fat diet or given an LXR agonist. ALA increased AMPK phosphorylation in the liver and in cultured liver cells, and dominant‐negative AMPK partially prevented ALA‐induced suppression of insulin‐stimulated SREBP‐1c expression. ALA also inhibited DNA‐binding activity and transcriptional activity of both specificity protein 1 and LXR. Conclusion: These results show that ALA prevents fatty liver disease through multiple mechanisms, and suggest that ALA can be used to prevent the development and progression of nonalcoholic fatty liver disease in patients with insulin resistance. (HEPATOLOGY 2008.)
What the future holds for gliptins

Gliptins have revolutionised the treatment of Type 2 Diabetes Mellitus, addressing the hyperglycemia through its effects on the alpha and beta cells of the pancreas. In this article,we review the extra-glycemic effects of gliptins on central nervous system, cardiovascular biology and the bone health and concerns regarding pancreatitis and pancreatic cancer.
Controlling Behaviors and Intimate Partner Violence Among Women in Spain: An Examination of Individual, Partner, and Relationship Risk Factors for Physical and Psychological Abuse

Intimate partner violence (IPV) has been linked to a broad range of negative consequences. Thus, early detection and prevention of behaviors associated with IPV is necessary to combat this global public health problem. Controlling behaviors (CBs) within the intimate context, including acts to constrain free mobility or access to friends and relatives, have been characterized as a moderate form of violence and may be an indicator of more severe IPV. Previous research in this field, however, has been primarily conducted in the United States. Accordingly, we lack knowledge of similar findings in other countries to draw more general conclusions about observed associations between these variables, and to identify underlying mechanisms. The current study analyzes the role of control within the Spanish context by examining its correlates, as well as the role and impact of CBs on psychological and physical violence. To achieve these objectives, we use data from the Spanish sample of the Violence Against Women Survey carried out by the European Union Agency for Fundamental Rights (N = 1,520 adult women). The results indicated that young women, women with a previous history of physical/sexual abuse during childhood, and women who have resided in Spain for fewer years are at greater risk of experiencing control within the context of an ongoing relationship. Partner risk factors included frequent episodes of drunkenness and general violence (i.e., violence outside of the home). In addition, control was more frequently reported among couples where the man was older than the woman. As hypothesized, women who reported CB by their partners were more likely to experience psychological and physical violence. These findings emphasize the importance of preventing CBs to avert the most severe forms of violence, and provides relevant information about the groups that could most benefit from these efforts.
Antiatherogenic Properties of Acetone Extract of Alpinia zerumbet Seeds

Oxidation of low-density lipoprotein (LDL) is the principal risk factor for the development of atherosclerosis. In this study, we used several methods to investigate the ability of the acetone extract from rhizomes, stems, leaves, flowers, pericarps and seeds of Alpinia zerumbet to inhibit atherosclerosis in vitro. The seed extract had the strongest activity against tyrosinase, pancreatic lipase (PL), 15-lipoxygenase (15-LO) and LDL oxidation activities (IC50 = 2.30 ± 0.02, 5.00 ± 0.07, 1.29 ± 0.07 and 15.40 ± 0.86 µg/mL, respectively), amongst all different parts. It also had similar effects to the positive controls. Most of the extracts showed partial agonistic properties towards estrogenic activity. Cholest-4-ene-3,6-dione, a steroid present only in the seed extract seems to be the compound responsible for these activities. The results showed that cholest-4-ene-3,6-dione had similar ability to curcumin and quercetin against PL and LDL oxidation (IC50 = 19.50 ± 1.17 and 16.12 ± 1.43 µg/mL, respectively). Furthermore, cholest-4-ene-3,6-dione (IC50 = 34.21 ± 1.31 µg/mL) had higher inhibition against 15-LO than quercetin (IC50 = 54.79 ± 1.12 µg/mL).
Exploring consumers' attitudes towards paper products that could be derived from transgenic plantations in Greece

This paper aims at exploring consumers' purchasing behaviour towards paper products that could be derived from transgenic plantations. Field interviews were conducted to a randomly selected sample of 205 consumers, who declared that they would buy such paper products. Principal Components Analysis indicated that the main factors affecting consumers' purchasing behaviour towards those products are potential environmental impacts of biotechnology use in forest trees, marketing issues relevant to paper products and product characteristics. Moreover, potential environmental and economic impacts mainly influence consumers' attitudes towards biotechnology use in forest trees. Through cluster techniques three groups of consumers with similar consumption behaviour were identified: a opportunists; b consumers with environmental concerns about biotechnology use; c consumers interested in marketing issues. Discriminant analysis was performed to predict cluster membership and a non-parametric test to profile each consumer group according to personal characteristics and attitude towards biotechnology use in forest trees.
Gold-Iron Oxide Catalyst for CO Oxidation: Effect of Support Structure

Gold-iron oxide (Au/FeOx) is one of the highly active catalysts for CO oxidation, and is also a typical system for the study of the chemistry of gold catalysis. In this work, two different types of iron oxide supports, i.e., hydroxylated (Fe_OH) and dehydrated iron oxide (Fe_O), have been used for the deposition of gold via a deposition-precipitation (DP) method. The structure of iron oxide has been tuned by either selecting precipitated pH of 6.7–11.2 for Fe_OH or changing calcination temperature of from 200 to 600 °C for Fe_O. Then, 1 wt. % Au catalysts on these iron oxide supports were measured for low-temperature CO oxidation reaction. Both fresh and used samples have been characterized by multiple techniques including transmission electron microscopy (TEM) and high-resolution TEM (HRTEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), X-ray absorption near edge structure (XANES) and temperature-programmed reduction by hydrogen (H2-TPR). It has been demonstrated that the surface properties of the iron oxide support, as well as the metal-support interaction, plays crucial roles on the performance of Au/FeOx catalysts in CO oxidation.
Cascading effect in bioprocessing—The impact of mild hypothermia on CHO cell behavior and host cell protein composition

A major challenge in downstream purification of monoclonal antibodies (mAb) is the removal of host cell proteins (HCPs). Previous studies have shown that cell culture conditions significantly impact the HCP content at harvest. However, it is currently unclear how process conditions affect physiological changes in the host cell population, and how these changes, in turn, cascade down to change the HCP profile. We examined how temperature downshift (TDS) to mild hypothermia affects key upstream performance indicators, that is antibody titre, HCP concentration and HCP species, across the cell culture decline phase and at harvest through the lens of changes in cellular behavior. Mild hypothermic conditions introduced on day 5 of fed‐batch Chinese hamster ovary (CHO) cell bioreactors resulted in a lower cell proliferation rate but larger percentages of healthier cells across the cell culture decline phase compared to bioreactors maintained at standard physiological temperature. Moreover, the onset of apoptosis was less evident in mild hypothermic cultures. Consequently, mild hypothermic cultures took an extra 5 days to reach an integral viable cell concentration (IVCC) and antibody yield similar to that of the control at standard physiological temperature. When cell viability dropped below 80%, mild hypothermic cell cultures had a reduced variety of HCP species by 36%, including approximately 44% and 27% lower proteases and chaperones, respectively, despite having similar HCP concentration. This study suggests that TDS may be a good strategy to provide cleaner downstream feedstocks by reducing the variety of HCPs and to maintain product integrity by reducing the number of proteases and chaperones.
Impact of the Mobile Phone on Junior High-School Students' Friendships in the Tokyo Metropolitan Area

The proportion of having keitai (Japanese mobile phone) has increased rapidly in young children. To research how junior high school students use their own keitai and to examine the impact of using it on their psychology, especially on their friendship, we recruited 651 students, grade 8, from five public junior high schools in the Tokyo metropolitan area. Each student participant completed a questionnaire that we had created. The response rates were 88.8% (n = 578) for participants. The proportion of having their own keitai was 49.3% (n = 285) and that of not having it was 50.7% (n = 293). We found that they used it much more frequently for e-mail than as a phone. Most of them exchanged e-mails between schoolmates, and more than a half of them exchanged e-mails more than 10 times a day. Sociable students estimated that their own keitai was useful for their friendship. But they experienced some insecurity or started staying up late at night engaged in e-mail exchanges, and they thought that they could not live without their own keitai. Our findings suggest that keitai having an e-mail function play a big part in the junior high-school students' daily life, and its impact on students' friendships, psychology, or health should be discussed among students to prevent keitai addiction.
Balloon mitral valvuloplasty in the elderly

Balloon mitral valvuloplasty has, over the last 15 years, become an established interventional procedure. For patients with pliable uncalcified mitral stenosis, dilatation with the Inoue balloon is the intervention of choice, offering results comparable to surgical commissurotomy.1 In the Western world, however, with the gradual extinction of rheumatic fever, patients with mitral stenosis are now almost exclusively elderly. Such patients tend to have calcified, thickened, and relatively immobile valves, often with significant subvalvar disease, and as such are theoretically unsuited to balloon valvuloplasty.2 3 But even a small increase in mitral valve orifice may be adequate to allow an elderly person to regain their independence; therefore some have advocated undertaking the interventional option at low risk, with only moderate expectations, rather than opting for mitral valve replacement, with its significant perioperative morbidity and mortality. But is this approach justified? In this issue of Heart , Sutaria and colleagues describe long term outcome for elderly patients undergoing balloon valvuloplasty at one high volume UK centre.4Patients considered unsuitable for surgery—in whom the decision to offer valvuloplasty was therefore in some respects straightforward—had a relatively poor, though not surprising, event free survival rate of 25% at five years. Among those considered suitable for surgical treatment, one year survival free of death or mitral valve replacement, and with improvement in New York Heart Association class by at least one grade, was 64%, falling to 36% at five years. By this stage, numbers were few. In the absence of a randomised trial of surgical versus interventional management of mitral stenosis in elderly patients (which is never likely to happen, and in which treatment arms could not be strictly comparable anyway5), mitral valvuloplasty would seem on this evidence to be a …
Investigating selected patient safety indicators using medical records data

Introduction: Medical errors in hospitals kill more people every year than AIDS, breast cancer and auto accidents combined. Widespread consensus exists that health care organizations can reduce patient injuries by improving the environment for safety from implementing different alternatives from technical and managerial improvements to considering medical record data. Considering the preventability of medical errors, the Agency for Healthcare Quality and Research (AHRQ) developed patient safety indicators (PSIs). This study analyzes the PSIs calculated in Alzahra Hospital of Isfahan. Materials and Methods: This study was conducted retrospectively using the inpatient medical record data of hospitalized patients in a six month period, from October 2010 to March 2011. An experienced team in the fields of medical record, health management and health information technology was involved in data reviewing. Based on a prior consultation and reviewing, some PSIs were selected. Indicators were calculated considering AHRQ guidelines. Excel software and hospital information system software were used. Results: Across all studied medical records of patients, out of 25,164 discharges, below measures were calculated. -8 Foreign Body cases (PSI 5) (0.31 per 1000). -30 Postoperative Hemorrhage or Hematoma cases (PS I9) (2.2 per 1000). -5 Accidental Puncture or Laceration cases (PSI 15) (0.3 per1000). -8 Complications of Anesthesia cases (PSI 1) (2.2 per 1000). -96 Selected Infections Due to Medical Care cases (PSI 7) (3.8 per1000). -17 cases of Postoperative Wound Dehiscence (PSI 14) (3.7per1000). -1 Birth Trauma – Injury to Neonate case, and (PSI 17) (1.7 per 1000). - 18 Obstetric Trauma – Cesarean Delivery cases (PSI 20) (40 per 1000) were flagged by studied PSIs developed by AHRQ. Conclusion: Comparing with the reported rates by other studies and AHRQ study in 2006, all of calculated indicators have inadequate condition; i.e. these are far from empirical estimated rates. The hospital administrators should be more sensitive to this issue and perform some improvement programs.
MSH6 and MUTYH Deficiency Is a Frequent Event in Early-Onset Colorectal Cancer

Purpose: Early-onset colorectal cancer (CRC) is suggestive of a hereditary predisposition. Lynch syndrome is the most frequent CRC hereditary cause. The MUTYH gene has also been related to hereditary CRC. A systematic characterization of these two diseases has not been reported previously in this population. Experimental Design: We studied a retrospectively collected series of 140 patients ≤50 years old diagnosed with nonpolyposis CRC. Demographic, clinical, and familial features were obtained. Mismatch repair (MMR) deficiency was determined by microsatellite instability (MSI) analysis, and immunostaining for MLH1, MSH2, MSH6, and PMS2 proteins. Germline MMR mutations were evaluated in all MMR-deficient cases. Tumor samples with loss of MLH1 or MSH2 protein expression were analyzed for somatic methylation. Germline MUTYH mutations were evaluated in all cases. BRAF V600E and KRAS somatic mutational status was also determined. Results: Fifteen tumors (11.4%) were MSI, and 20 (14.3%) showed loss of protein expression (7 for MLH1/PMS2, 2 for isolated MLH1, 3 for MSH2/MSH6, 7 for isolated MSH6, and 1 for MSH6/PMS2). We identified 11 (7.8%) germline MMR mutations, 4 in MLH1, 1 in MSH2, and 6 in MSH6. Methylation analysis revealed one case with somatic MLH1 methylation. Biallelic MUTYH mutations were detected in four (2.8%) cases. KRAS and BRAF V600E mutations were present in 39 (27.9%) and 5 (3.6%) cases, respectively. Conclusions: Loss of MSH6 expression is the predominant cause of MMR deficiency in early-onset CRC. Our findings prompt the inclusion of MSH6 and MUTYH screening as part of the genetic counseling of these patients and their relatives. Clin Cancer Res; 16(22); 5402–13. ©2010 AACR.
A modified bat algorithm for the Quadratic Assignment Problem

Quadratic Assignment Problem (QAP) is a discrete search space problem where one has to find the perfect feasible permutation of locations which minimizes the objective function. This paper solves the quadratic assignment problem using bat algorithm. Bat algorithm cannot be directly applied for solving QAP as it generates a solution for continuous search space problems. Therefore, we use a heuristic rule called Smallest Position Value (SPV) to enable our algorithm for finding solutions for sequencing problems. The modified algorithm completely outperforms the particle swarm optimization algorithm in all the cases considered.
Effect of chitosan ethers on fresh state properties of lime mortars

The fresh state properties of mortars are eminently important since determine the material workability and also have a great influence on its hardened state characteristics. In this paper, the behaviour of fresh lime mortars modified by etherified derivatives of chitosan (hydroxypropylchitosan (HPCH) and carboxymethylchitosan (CMCH)) is assessed with the purpose of exploring a new application of such derivatives as lime mortar admixtures. The rheological parameters (relative yield stress, consistency coefficient and fluidity index) and viscoelastic properties were correlated with flow table tests, relative density measurements, water retention abilities of mortars and air content in mortars. Results were seen to be strongly dependent on substituents of the chitosan. Non-ionic derivative (HPCH) had a plasticizing influence on the mortars; the ionic CMCH showed the thickening effect. The effect of chitosan ethers was found to be dosage-dependent. CMCH had low impact on water retention, while HPCH displayed high water retention capability. It was concluded, that the ionic derivative (CMCH) is very similar by its viscosity enhancing effect to starch ether.
The ImpacT of DIfferenT VecTor Space moDelS anD SupplemenTary TechnIqueS on ruSSIan SemanTIc SImIlarITy TaSk

This paper presents a system for determining semantic similarity between words that was an entry for the Dialog 2015 Russian semantic similarity competition. The system introduced is primary based on word vector models, supplemented with various other methods, both corpusand dictionary-based. In this paper we compare performance of two methods for building word vectors (word2vec and GloVe), evaluate how performance
A behavioral approach to worm detection

This paper presents a new approach to the automatic detection of worms using behavioral signatures. A behavioral signature describes aspects of any particular worm's behavior that are common across the manifestations of a given worm and that span its nodes in temporal order. Characteristic patterns of worm behaviors in network traffic include 1) sending similar data from one machine to the next, 2) tree-like propagation and reconnaissance, and 3) changing a server into a client. These behavioral signatures are presented within the context of a general worm propagation model. Taken together, they have the potential to detect entire classes of worms including those which have yet to be observed. This paper introduces the concept of an network application architecture (NAA) as a way to distribute network applications. An analysis shows that the choice of NAA impacts the sensitivity of behavioral signatures. An NAA that satisfies certain constraints significantly improves worm detection sensitivity. Mathematical models of traffic flow, NAAs, worm propagation, and worm detection provide a context for the entire discussion.