Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of the Peptidase Domain of Streptococcus ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway*

ComA of Streptococcus is a member of the bacteriocin-associated ATP-binding cassette transporter family and is postulated to be responsible for both the processing of the propeptide ComC and secretion of the mature quorum-sensing signal. The 150-amino acid peptidase domain (PEP) of ComA specifically recognizes an extended region of ComC that is 15 amino acids in length. It has been proposed that an amphipathic α-helix formed by the N-terminal leader region of ComC, as well as the Gly-Gly motif at the cleavage site, is critical for the PEP-ComC interaction. To elucidate the substrate recognition mechanism, we determined the three-dimensional crystal structure of Streptococcus mutans PEP and then constructed models for the PEP·ComC complexes. PEP had an overall structure similar to the papain-like cysteine proteases as has long been predicted. The active site was located at the bottom of a narrow cleft, which is suitable for binding the Gly-Gly motif. Together with the results from mutational experiments, a shallow hydrophobic concave surface of PEP was proposed as a site that accommodates the N-terminal helix of ComC. This dual mode of substrate recognition would provide the small PEP domain with an extremely high substrate specificity.
Assessing price integration and trade policy in the U.S. catfish market

ABSTRACT In 2003, the United States adopted anti-dumping tariffs for Vietnamese catfish products entering the country. This study examines how these tariffs have impacted the price relationship between domestically produced and imported catfish products. Cointegration tests confirm a long-run price relationship between domestic and imported catfish, which has persisted despite the anti-dumping tariffs. However, imports are composed of catfish from Vietnam and other countries, with only the former subjected to tariffs. Results from vector error correction models suggest that Vietnamese catfish prices do not significantly influence domestic prices. Conversely, the price of catfish from countries other than Vietnam continues to impact prices received by domestic catfish farmers and processors. The domestic catfish industry is still affected by lower-priced imports from countries other than Vietnam, although some of these may be transshipments that truly originate in Vietnam. This research methodology could be adapted to investigate trade and price interactions among other aquacultured species, which will become increasingly important as global aquaculture expands.
Embedded InN dot-like structure within InGaN layers using gradient-Indium content in nitride-based solar cell

The novel design of embedded InN dot-like structure within InGaN was useful as an absorption layer in photovoltaic (PV) cells. We constructed the simulation model by employing the commercial software APSYS® and integrating the absorption coefficient of thin InN materials fabricated by metal organic vapor deposition (MOCVD). The model of simulating gradient Indium content of InGaN used as transition interface between InN and GaN was investigated. The results exhibit utilizing the effective variation of Indium content and suitable thickness to approach the optimal characteristic of hybrid InN/InGaN structure within solar cells shall be anticipated to enhance the performance of current nitride-based solar cells.
Diversity, Inclusion, and Commitment in Organizations: International Empirical Explorations

University of Southern California Research on social demography in the workplace indicates that people from diverse groups commonly find themselves excluded from networks of information and opportunity. In today’s global economy, diversity needs to be examined from an intra-national as well as international perspective. Utilizing social identity and intergroup theories and focusing on the inclusion-exclusion construct, this article formulates a conceptual model of the relationship between diversity, inclusion and commitment and tests it in two samples drawn from high-tech companies in the U.S. and in Israel. The results support the applicability of the model across the two cultures, but the role of diversity in the model proves to be more limited than hypothesized. The results suggest that, while the context of diversity and its specific categories differ across cultures, there are similarities in the associated experience of exclusion.
Contribution and interaction of the low‐density lipoprotein cholesterol to high‐density lipoprotein cholesterol ratio and triglyceride to diabetes in hypertensive patients: A cross‐sectional study

Hypertension is one of the most significant risk factors for diabetes. The present study aimed to investigate the associations of lipid profiles, including the ratio of low‐density lipoprotein cholesterol (LDL‐C)‐to‐high‐density lipoprotein cholesterol (HDL‐C) and triglyceride (TG) levels, as well as their interactions, with type 2 diabetes in hypertensive patients.
Enhanced Disclosure of Other Comprehensive Income and Increased Usefulness of Net Income: The Implications of Accounting Standards Update 2011-05

Accounting Standards Update (ASU) 2011–05 eliminates the option to present other comprehensive income (OCI) in the statement of changes in stockholders’ equity. This study empirically investigates whether this mandatory change of OCI presentation format achieves FASB's stated objective of improving the transparency of financial reporting. First, ASU 2011–05 is found to greatly reduce the continuity of OCI from one period to the next. As OCI items are transitory in nature, the increased OCI volatility makes firms’ inherent risk more transparent to investors. Second, ASU 2011–05 is found to significantly increase the ability of net income to influence stock prices. As OCI and net income are intertwined, the more salient presentation of OCI enables investors to better interpret earnings. Supporting FASB's position that OCI items need to be more prominently displayed, these findings suggest that the new standard improves transparency and usefulness of the reported OCI information.
Predicting drought tolerance from slope aspect preference in restored plant communities

Summary Plants employ strategies of tolerance, endurance, and avoidance to cope with aridity in space and time, yet understanding the differential importance of such strategies in determining patterns of abundance across a heterogeneous landscape is a challenge. Are the species abundant in drier microhabitats also better able to survive drought? Are there relationships among occupied sites and temporal dynamics that derive from physiological capacities to cope with stress or dormancy during unfavorable periods? We used a restoration project conducted on two slope aspects in a subwatershed to test whether species that were more abundant on more water‐limited S‐facing slopes were also better able to survive an extreme drought. The attempt to place many species uniformly on different slope aspects provided an excellent opportunity to test questions of growth strategy, niche preference, and temporal dynamics. Perennial species that established and grew best on S‐facing slopes also had greater increases in cover during years of drought, presumably by employing drought tolerance and endurance techniques. The opposite pattern emerged for annual species that employed drought‐escape strategies, such that annuals that occupied S‐facing slopes were less abundant during the drought than those that were more abundant on N‐facing slopes. Our results clarify how different functional strategies interact with spatial and temporal heterogeneity to influence population and community dynamics and demonstrate how large restoration projects provide opportunities to test fundamental ecological questions.
1-Tetradecanol complex: therapeutic actions in experimental periodontitis.

BACKGROUND The present study was planned to investigate the therapeutic actions of 1-tetradecanol complex (1-TDC), a novel monounsaturated fatty acid mixture, in established periodontitis in rabbits. METHODS Periodontitis was initiated in 18 New Zealand White rabbits using ligatures around mandibular second premolars, followed by topical Porphyromonas gingivalis application (10(9) colony forming units). After 6 weeks of disease induction (phase 1), three animals were sacrificed to assess the established periodontitis level. P. gingivalis application was discontinued, and the remaining 15 animals continued with topical treatment of 1-TDC (100 mg/ml; n = 5) or placebo (n = 5) or no treatment (n = 5) for an additional 6 weeks (phase 2). Mandibular block sections obtained after euthanasia were decalcified and embedded in paraffin. In addition to the macroscopic analyses, hematoxylin and eosin-stained sections were used to study cellular inflammatory infiltrate and quantitative histomorphometry. Tartrate-resistant acid phosphatase and osteocalcin were used to identify osteoclastic and osteoblastic activity, respectively. RESULTS P. gingivalis application resulted in periodontal disease with gingival inflammation and bone loss (30% compared to baseline) at 6 weeks. Treatment with 1-TDC stopped the progression of the disease and resulted in a significant reduction in the macroscopic periodontal inflammation, attachment, and bone loss (10.1% +/- 1.8%), whereas periodontal disease progressed in the untreated and placebo groups (P <0.05). Histologic assessment and histomorphometric measurements demonstrated that 1-TDC inhibited inflammatory cell infiltration and osteoclastic activity (P <0.05). CONCLUSION The findings suggest that topical application of cetylated monounsaturated fatty acid complex (1-TDC) is a potential therapeutic approach in controlling the progression of chronic periodontal disease.
Genes for the Type IV Secretion System in an Intracellular Symbiont, Wolbachia, a Causative Agent of Various Sexual Alterations in Arthropods

ABSTRACT Wolbachia species are intracellular bacteria known to cause reproductive abnormalities in their hosts. In this study, we identified Wolbachia genes encoding homologs to the type IV secretion system by which many pathogenic bacteria secrete macromolecules. The genes identified encoded most of the essential components of the secretion system and were cotranscribed as an operon.
Spatial/temporal correlation of BOLD and optical intrinsic signals in humans

Comparing the BOLD signal with electrophysiological maps and other perfusion‐dependent signals, such as the optical intrinsic signal (OIS), within subjects should provide insight into the etiology of the BOLD signal. Tongue activations were compared in five human subjects using BOLD fMRI, 610‐nm OIS, and the electrocortical stimulation map (ESM). Robust fMRI activations centered on the lateral inferior aspect of the central sulcus and extended into pre‐ and post‐central gyri, adjacent to ESM tongue loci. OIS and fMRI maps colocalized, although optical responses were spatially larger (P < .001 across multiple thresholds) and contained more gyral components. The timecourses of the fMRI and OIS signals were similar, appearing within 2.5 s and peaking 6–8 s after task onset. Although many processes contribute to increased 610‐nm reflectance, optical spectroscopy and fluorescent dye imaging suggest that a significant part of this signal is due to a concomitant decrease in deoxyhemoglobin and increase in oxyhemoglobin concentrations. The spatial/temporal correlation of BOLD and the positive 610‐nm response within subjects suggests that the two signals may share similar etiologies. The OIS/fMRI inconsistencies may be due to cell swelling and light‐scattering contributions to OIS and fMRI sensitivity. This study also demonstrates that fMRI maps do not precisely colocalize with ESM, rather they emphasize changes in adjacent venous/sulcal structures. Magn Reson Med 47:766–776, 2002. © 2002 Wiley‐Liss, Inc.
Transcutaneous Electrical Stimulation of Subjective Tinnitus

Aim: The effect of the transcutaneous application of the electrical stimulus on tinnitus perception has been reviewed in a placebo-controlled, randomized and comparative analysis to eventually determine the outcome of the therapeutic role of the therapy. Method: There are 42 patients who were randomized into 2 groups according to their order of admission. Group A consists of 31 patients who were subjected to transcutaneous electrical stimulation 3 times a week for 1 month. Group B includes 11 patients who had electrical stimulus attachment but where no stimulus was given (placebo group). The stimulator is a custom-made device which generates direct and alternative current in 10–200 Hz frequency. An alternative low-frequency (not >100 Hz) pulsed current was used for tinnitus therapy through a preauricular skin electrode. The amplitude of stimulus ranged between 50 and 2,000 mA. The pulse frequency was 30 Hz. Each session lasted for 25 min for both groups. Statistical analysis was performed. Result: The rate of improvement following the therapy was 42.8% (18/42) in the electrical therapy group and 28.5% (4/14) in the placebo group. Conclusion: Electrical suppression of the tinnitus does not offer a promising outcome for patients with tinnitus in the presented study.
Naturally occurring tyrosinase inhibitors: mechanism and applications in skin health, cosmetics and agriculture industries

Tyrosinase is a copper‐containing enzyme, which is widely distributed in microorganisms, animals and plants and is a key enzyme in melanin biosynthesis, involved in determining the color of mammalian skin and hair. In addition, unfavorable enzymatic browning of plant‐derived foods by tyrosinase causes a decrease in nutritional quality and economic loss of food products. The inadequacy of current conventional methods to prevent tyrosinase action encourages researchers to seek new potent tyrosinase inhibitors for food and cosmetics.
AppTechMiner: Mining Applications and Techniques from Scientific Articles

This paper presents AppTechMiner, a rule-based information extraction framework that automatically constructs a knowledge base of all application areas and problem solving techniques. Techniques include tools, methods, datasets or evaluation metrics. We also categorize individual research articles based on their application areas and the techniques proposed/improved in the article. Our system achieves high average precision (~82%) and recall (~84%) in knowledge base creation. It also performs well in application and technique assignment to an individual article (average accuracy ~66%). In the end, we further present two use cases presenting a trivial information retrieval system and an extensive temporal analysis of the usage of techniques and application areas. At present, we demonstrate the framework for the domain of computational linguistics but this can be easily generalized to any other field of research. We plan to make the codes publicly available.
RITUXIMAB AND TOCILIZUMAB FOR THE TREATMENT OF RHEUMATOID ARTHRITIS

Objectives: The aim of this study was to evaluate the efficacy and safety of rituximab and tocilizumab compared with adalimumab, etanercept, and infliximab, in patients with rheumatoid arthritis not responding to first-line treatment, and to compare the efficacy and safety of rituximab versus tocilizumab in patients not responding to anti-tumor necrosis factor α (anti-TNF) therapy. Methods: A literature search of randomized controlled trials, controlled clinical trials, and systematic reviews was performed to evaluate efficacy and safety of rituximab and tocilizumab. Results: Twenty-four RCTs were included in this systematic review with 6,357 participants; 3,450 treated with biological DMARD and 2,907 with standard care. In patients not responding to first-line treatment, rituximab shows lower response rate in at least 50 percent improvement in the American College of Rheumatology criteria (ACR50) and ACR70 compared with etanercept, at 6 months of follow-up. Tocilizumab shows higher ACR70 response rate compared with infliximab, at the same follow-up time. Other results showed no significant differences. Indirect comparisons between rituximab and tocilizumab in patients not responding for at least one anti-TNF, shows higher ACR20 response rate for tocilizumab at 6 months of follow-up. Regarding safety, adalimumab and etanercept were associated with significant fewer withdrawals due to adverse events compared with infliximab. Conclusions: Considering efficacy, safety, and the availability of 3 anti-TNFs in the National Medicines Formulary (adalimumab, etanercept, and infliximab), it seems appropriate to remove infliximab from the coverage, and introduce tocilizumab for patients not responding for at least one anti-TNF.
Disparities in Potentially Preventable Hospitalizations: Near‐National Estimates for Hispanics

OBJECTIVE To obtain near-national rates of potentially preventable hospitalization (PPH)-a marker of barriers to outpatient care access-for Hispanics; to examine their differences from other race-ethnic groups and by Hispanic national origin; and to identify key mediating factors. DATA SOURCES/STUDY SETTING Data from all-payer inpatient discharge databases for 15 states accounting for 85 percent of Hispanics nationally. STUDY DESIGN Combining counts of inpatient discharges with census population for adults aged 18 and older, we estimated age-sex-adjusted PPH rates. We examined county-level variation in race-ethnic disparities in these rates to identify the mediating role of area-level indicators of chronic condition prevalence, socioeconomic status (SES), health care access, acculturation, and provider availability. PRINCIPAL FINDINGS Age-sex-adjusted PPH rates were 13 percent higher among Hispanics (1,375 per 100,000 adults) and 111 percent higher among blacks (2,578) compared to whites (1,221). Among Hispanics, these rates were relatively higher in areas with predominantly Puerto Rican and Cuban Americans than in areas with Hispanics of other nationalities. Small area variation in chronic condition prevalence and SES fully accounted for the higher rates among Hispanics, but only partially among blacks. CONCLUSIONS Hispanics and blacks face higher barriers to outpatient care access; the higher barriers among Hispanics (but not blacks) seem mediated by SES, lack of insurance, cost barriers, and limited provider availability.
Isolation and characterization of DNA sequences that are specifically bound by wild-type p53 protein

Wild-type p53 was shown to function as a transcription factor. The N-terminal region of the protein contains the transcription activation domain, while the C terminus is responsible for DNA binding. Localization of the DNA-binding domain of the p53 protein to the highly conserved carboxy-terminal region suggests that the interaction of p53 with DNA is important for its function. We have developed a strategy for studying the DNA sequence specificity of p53-DNA binding that is based on random sequence selection. We report here on the isolation of murine genomic DNA clones that are specifically bound by the wild-type p53 protein but are not bound by mutant p53 protein forms. The isolated p53 target gene contains the unique DNA-binding sequence GACACTGGTCACACTTGGCTGCTTAGGAAT. This fragment exhibits promoter activity as measured by its capacity to activate transcription of the chloramphenicol acetyltransferase reporter gene. Our results suggest that p53 directly binds DNA and functions as a typical transcription factor.
Role of Lys335 in the metastability and function of inhibitory serpins

The native form of inhibitory serpins (serine protease inhibitors) is not in the thermodynamically most stable state but in a metastable state, which is critical to inhibitory functions. To understand structural basis and functional roles of the native metastability of inhibitory serpins, we have been characterizing stabilizing mutations of human α1‐antitrypsin, a prototype inhibitory serpin. One of the sites that has been shown to be critical in stability and inhibitory activity of α1‐antitrypsin is Lys335. In the present study, detailed roles of this lysine were analyzed by assessing the effects of 13 different amino acid substitutions. Results suggest that size and architect of the side chains at the 335 site determine the metastability of α1‐antitrypsin. Moreover, factors such as polarity and flexibility of the side chain at this site, in addition to the metastability, seem to be critical for the inhibitory activity. Substitutions of the lysine at equivalent positions in two other inhibitory serpins, human α1‐antichymotrypsin and human antithrombin III, also increased stability and decreased inhibitory activity toward α‐chymotrypsin and thrombin, respectively. These results and characteristics of lysine side chain, such as flexibility, polarity, and the energetic cost upon burial, suggest that this lysine is one of the structural designs in regulating metastability and function of inhibitory serpins in general.
The Mediational Effect of Weight Self-Stigma in the Relationship between Blatant and Subtle Discrimination and Depression and Anxiety

Abstract Obesity may be considered a social stigma. In addition, people with obesity are frequently aware of stigma directed at others who have a similar weight and come to think stigmatized thoughts about themselves. Our study focused specifically on how blatant and subtle discrimination and weight self-stigma are related to depression and anxiety in people with obesity. The sample comprised 170 participants from the Clinical Nutrition Unit of the “Hospital de Valme” (Seville, Spain). The Weight Self-Stigma Questionnaire, the Multidimensional Perceived Discrimination Scale, and the Hospital Anxiety and Depression Scale were used. It was found that blatant and subtle discrimination and weight self-stigma were positively related to depression (.31, .38, and .45 respectively) and anxiety (.30, .36, and .49 respectively; all ps < .01). The path analysis conducted showed that there was a mediational effect of weight self-stigma between blatant (β = .36) and subtle discrimination (β = .40) and depression (β = .24) and anxiety (β = .49; all ps < .01). According to these results, it can be said that weight self-stigma was a full mediator in the model found because the relationships between the independent and the dependent variables were non-significant. Finally, results are discussed in the frame of the obesity stigma literature, and some clinical implications of the results of the study are suggested.
Split-Rib Cranioplasty

Cranioplasty using a synthetic material is less than ideal, especially if there is a history of infection at the defect site. Split-rib cranioplasty is a practical approach even in patients with a positive history of infection at or around the defect. We briefly review the historical background of split-rib cranioplasty and report our experience with this procedure in 12 patients. Forty-two pieces of rib, with an average length of 13 cm, were used for reconstruction. We had only 1 complication—a pneumothorax following removal of the rib graft. The follow-up period ranged from three to thirty-six months. All patients had complete regeneration of the donor rib and solid protection of the brain.