Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets

Reduced or simplified amino acid alphabets group the 20 naturally occurring amino acids into a smaller number of representative protein residues. To date, several reduced amino acid alphabets have been proposed, which have been derived and optimized by a variety of methods. The resulting reduced amino acid alphabets have been applied to pattern recognition, generation of consensus sequences from multiple alignments, protein folding, and protein structure prediction. In this work, amino acid substitution matrices and statistical potentials were derived based on several reduced amino acid alphabets and their performance assessed in a large benchmark for the tasks of sequence alignment and fold assessment of protein structure models, using as a reference frame the standard alphabet of 20 amino acids. The results showed that a large reduction in the total number of residue types does not necessarily translate into a significant loss of discriminative power for sequence alignment and fold assessment. Therefore, some definitions of a few residue types are able to encode most of the relevant sequence/structure information that is present in the 20 standard amino acids. Based on these results, we suggest that the use of reduced amino acid alphabets may allow to increasing the accuracy of current substitution matrices and statistical potentials for the prediction of protein structure of remote homologs. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Dynamic modeling of modular multilevel DC/DC converters for HVDC systems

This paper presents the first dynamic model of the DC-MMC, a new class of modular multilevel single-stage dc/dc converters aptly suited for HVDC systems. A state-space model for a single string of the DC-MMC is developed and validated by comparing with time-domain simulation results from a comprehensive switched converter model. The developed averaged model is utilized to investigate submodule capacitor voltage balancing characteristics of the DC-MMC. In particular it is demonstrated that, unlike the dc/ac modular multilevel converter, direct ac modulation of the DC-MMC is not sufficient to keep capacitor voltages balanced. The developed model is also used to propose and validate a supplemental controller that suppresses unwanted second and third harmonic circulating ac currents within the DC-MMC.
Management of Neglected Periorbital Squamous Cell Carcinoma Requiring Orbital Exenteration

AbstractWith its perineural invasion capacity, periorbital squamous cell carcinoma (SCC) may easily invade orbital structures. When SCC invades the orbital musculature or the orbit itself, orbital exenteration, one of the most disfiguring operations on the face, is required. We reviewed elderly patients with periorbitally localized SCC requiring orbital exenteration to evaluate reconstructive options and survival. A chart review of patients’ records was conducted to identify all patients older than 65 years with periorbital malignancy requiring orbital exenteration from 2006 to 2011. A total of 9 patients who met the criteria were included in the study. The mean age at surgery was 77 ± 6.7 years, and the mean defect size was 74.2 cm2. All patients had a similar history of late presentation to a doctor because of hesitation to undergo surgery. The temporoparietal fascia flap, galeal flap, free gracilis flap, and free vastus lateralis musculocutaneous flap were the treatment options for reconstruction of the defects. All patients died during follow-up, and the mean survival was 15.7 months (range, 6–36 months). Only 2 of them had relapse before the death. Our small series suggest that elderly patients with periorbital SCC requiring orbital exenteration may not have enough survival to relapse because of the death from different causes without relapse or any sign of spreading cancer. Also, prolonged surgery with free flap reconstruction may increase the risk of postoperative intensive care unit requirement. Because local flaps may work very well for reconstructing the orbital exenteration defects, free flap option should be kept for selected cases.
MODELING THE PHILLIPS CURVE IN CHINA: A NONLINEAR PERSPECTIVE

This paper investigates the nonlinear dynamics of the inflation–output type of Phillips curve based on a multiple-regime smooth transition regression model using data from China. The empirical results indicate significant nonlinearities in China's Phillips curve. The relationship between inflation and output can be modeled by a four-regime smooth transition regression model in which the responses of inflation to output depend on both inflation and economic growth rates. The inflation–output type Phillips curve may be positively sloped, negatively sloped, or even vertical in the short term, depending on different business cycles. Furthermore, we analyze business cycle fluctuations based on the nonlinear Phillips curve, indicating a coexisting zone of stable inflation rate and rapid growth rate.
NF-KappaB Independent Activation of a Series of Proinflammatory Genes by Hydrogen Sulfide

A stress response has the potential to induce greater resistance to subsequent stress damage. We tested whether hydrogen sulfide (H2S), an important signaling molecule, also used therapeutically, and known for detrimental effects, might induce a protective stress response. Therefore, the response of fibroblast-like synoviocytes (FLS) treated with sodium hydrosulfide and mice exposed to H2S were examined. In both cases a profound and long lasting induction of the stress-response could be detected. However, despite the sustained presence of large levels of HO-1 and HSP-70, proinflammatory effects of exposure to IL-1β or H2S itself were not ameliorated. On the contrary, at H2S concentrations significantly lower than 10 ppm—the current maximal allowable concentration of H2S in many countries—COX-2, IL-8, IL-1α, IL-1β and TNFα were dose dependently elevated. Importantly, in FLS, short-term exposure to H2S resulted in the activation of all three MAPK. In addition, mitochondrial activity was also significantly impaired at relatively low H2S concentrations. The transcription factor NF-κB is essential for the activation of most proinflammatory genes. However, the data presented imply that H2S activates proinflammatory genes in FLS through non-NF-κB-dependent pathways. Stress proteins reportedly act by blocking NF-κB activation, a mechanism that would explain the inability of stress proteins to prevent H2S mediated inflammatory processes. The presented data, showing MAPK activation, NF-κB-independent activation of a number of proinflammatory genes and mitochondrial damage, help to provide a better understanding of the biological and pathophysiological effects of exposure to H2S.
Protein kinase and specific phosphate acceptor proteins associated with tupaia herpesvirus

A protein kinase activity was found to be associated with tree shrew (tupaia) herpesvirus. The protein kinase was characterized with respect to its requirements for enzymatic activity. A divalent cation such as Mg2+ or Mn2+ was necessary as well as ATP as the phosphate donor. Distinct tupaia herpesvirus polypeptides (molecular weights of 100,000 [100K], 82K, and 53K) were found to be phosphate acceptor proteins when 5 mM Mg2+ was used. At a higher Mg2+ concentration (20 mM), additional viral proteins (220K, 71K, 31K, and 20K) were phosphorylated. The viral phosphoproteins were analyzed by chemical and enzymatic hydrolyses. The predominant sites of phosphorylation were the beta-OH groups of the serine and threonine residues of these tupaia herpesvirus proteins. Kinase activity was not stimulated by cyclic nucleoside monophosphates. Endogenously added proteins did not enhance protein kinase activity. Protein kinase activity was inhibited by 5'-p-fluorosulfonylbenzoyladenosine.
Stereotypes and Their Consequences for Women as Leaders in Higher Education Administration.

iv DEDICATION . vi ACKNOWLEDGEMENTS . vii CHAPTER ONE: Introduction . 1 Statement of the Problem . 3 Significance of the Problem . 6 Purpose of the Study . 8 Research Questions . 9 Theoretical and Conceptual Frameworks . 9 Significance of the Study . 11 CHAPTER TWO: Review of the Literature . 14 Stereotypes . 14 Evidence of Stereotypes . 18 Gender Stereotypes . 21 The Persistence of Gender Stereotypes . 25 Women and Work . 29 Gender Roles, Stereotyping, and Discrimination . 30 Gender and Occupational Stereotyping . 31 Gender Discrimination . 34 Differences in Opportunity and Career Advancement for Women . 38 Entry into the Workplace . 39
The Impact of CRM Infrastructural and Cultural Resources and Capabilities on Business Performance: An Application of the Resource-based View in the Mobile Telecommunications Industry

Based on the Resource-Based View (RBV) literature, this study aims at developing and implementing a novel and comprehensive model so as to measure the effect of CRM resources on CRM capabilities and the effect of the latter on business performance. CRM resources are defined as infrastructural CRM resources (i.e. technological resources, human resources, and organizational resources), and cultural CRM resources (i.e. customer orientation, learning orientation, and result orientation). CRM capabilities are measured through an organization’s customer interaction capability, customer relationship upgrading capability, and customer win-back capability. As for performance, this study measures business performance comprehensively from financial and marketing perspectives. Although the results indicate that CRM infrastructural resources has a positive and direct effect on CRM capabilities, the effect of customer orientation culture and learning orientation culture on CRM capabilities was significantly stronger. Further, the results indicate the CRM capabilities significantly and positively affect business performance from marketing and financial standpoints. However, the effect of CRM capabilities on marketing performance was found to be stronger than effect on financial performance and marketing performance was found to partially mediate the relationship between CRM capabilities and financial performance.
Successful liver transplantation for Budd‐Chiari syndrome in a patient with paroxysmal nocturnal hemoglobinuria treated with the anti‐complement antibody eculizumab

Paroxysmal nocturnal hemoglobinuria (PNH) is a rare, acquired hemolytic anemia caused by somatic mutations in the phosphatidylinositol glycan‐complementation class A gene and the resulting absence of a key complement regulatory protein, CD59. Affected red blood cells in patients with PNH undergo intravascular complement‐mediated lysis with resulting anemia, hemoglobinuria, and venous thromboses. Hepatic venous outflow thrombosis [Budd‐Chiari syndrome (BCS)] is especially common in PNH patients and often fatal. The few case reports of outcomes in patients undergoing liver transplant for BCS secondary to PNH detail instances of recurrent BCS as well as early thrombotic portal vein occlusion and hepatic artery thrombosis requiring retransplantation. PNH is therefore generally considered a contraindication to liver transplantation. Here we present the first report of a patient with PNH and BCS undergoing successful liver transplantation while receiving eculizumab, a humanized monoclonal antibody that blocks the activation of the terminal complement at C5. Liver Transpl 15:540–543, 2009. © 2009 AASLD.
Infant care practices in rural China and their relation to prenatal care utilisation

Abstract Studies describing postpartum childcare practices and the influence of prenatal care on infant care outcomes in rural China are scarce. This study looked at data for 1479 women who had given birth during the preceding 2 years (median age of the child was 8 months). Data were available from a Knowledge, Attitude and Perception cross-sectional survey collected from 2001 to 2003, after a prenatal care intervention in Anhui County, China, with a response rate of 97%. Prenatal care utilisation was categorised using the Adequacy of Prenatal Care Utilisation index. Logistic regression was used to study the association between prenatal care utilisation and infant care practices. Mothers' uptake of breastfeeding, introduction of milk formula, cereal/porridge, meat and uptake of any immunisation were found to be in accordance with national recommendations. Intermediate prenatal care uptake was positively associated with never breastfeeding and early introduction of cereal/porridge. Inadequate care was positively associated with never breastfeeding, early introduction of milk formula and cereal/porridge, and early start of work after delivery. Initiation to prenatal care after the third month was positively associated with early introduction of milk formula and cereal/porridge. Having no prenatal care was positively associated with never breastfeeding and early introduction of milk formula. Mothers' uptake of infant care practices in this population was largely in accordance with national recommendations. Women with less than adequate utilisation of prenatal care and those who had initiated prenatal care late were less likely to follow recommendations on infant care.
Levels of C-Reactive Protein and Protein C in Periodontitis Patients with and without Cardiovascular Disease

Since periodontitis is a chronic and inflammatory disease, a number of hypotheses have proposed that it has an etiological or modulating role in cardiovascular disease (CVD). This study aimed to ascertain the changes in the plasma levels of C-reactive protein (CRP) and protein C (PC), a natural anticoagulant also having an anti-inflammatory effect, in patients who have mild-to-severe periodontitis with or without CVD. The test group consisted of 26 patients with CVD and chronic periodontitis and the control group consisted of 26 patients with chronic periodontitis and no systemic disease. In both groups Community Periodontal Index of Treatment Needs scores were recorded and blood samples were collected. CRP levels were significantly high and PC activity was significantly low in the test group compared to the control group (p < 0.001). There was a negative correlation between tooth loss and PC and between CRP and PC. How PC is affected by the inflammatory events and its association with CRP is an active area of investigation.
Comparing penile measurements in normal and erectile dysfunction subjects.

INTRODUCTION With the increase in penile augmentation procedures it becomes important to assess what is the normal erect penile size in both potent men and men with erectile dysfunction (ED). AIM The aim of this work is to define the average stretched penile size in normal men and ED patients. MAIN OUTCOME MEASURES Penile length and girth. METHODS This study included 1,027 adult men presenting to a university hospital outpatient clinic. Two groups of patients were included in this research work. Group I comprises normal adult men (949) and Group II, ED patients (78). There were no differences of race, age, height, and weight. Penile length and girth were measured using a tape measure and rigid ruler in the fully stretched states in both groups. All penile measurements were performed by the same physician. RESULTS In normal men (Group I) the mean of the fully stretched length was 12.9 +/- 1.9 cm and the mean of the fully stretched girth was 8.9 +/- 0.9 cm. In ED patients (Group II), the mean of the fully stretched length was 11.2 +/- 1.5 cm and the mean of fully stretched girth was 8.8 +/- 0.8 cm. Comparing the mean of fully stretched penile lengths in both groups revealed statistical significant difference (P < 0.001) between them, whereas comparing the mean of fully stretched penile girths in both groups revealed statistical nonsignificant difference (P = 0.474) between them. There were significant positive correlations between fully stretched penile lengths and fully stretched penile girths in both groups. CONCLUSION The average of fully stretched penile length in normal potent men is 12.9 cm, whereas the patients with ED tend to have significantly shorter penises (11.2 +/- 1.5 cm).
Frequency of precursor cells against the enzyme β‐galactosidase An estimate of the BALB/c strain antibody repertoire

A method has been developed for detecting anti‐β‐galactosidase antibodies after isoelectric focusing in thin layers of polyacrylamide gel. By “staining” with wild‐type enzyme, all antibodies against β‐galactosidase are detected, while a subset of antibodies able to activate a mutant enzyme is detected by staining with that enzyme.
Expression of intermediate filament desmin and vimentin in the human fetal heart

The intermediate filament (IF) desmin provides support for contractile machinery in muscle cells, and vimentin plays an important role in maintaining the stability of mesenchymal cells and in signal transduction. However, development of IFs in heart tissue during intrauterine life in human is not well established.
Three-dimensional computer-aided diagnosis scheme for detection of colonic polyps

We have developed a three-dimensional (3-D) computer-aided diagnosis scheme for automated detection of colonic polyps in computed tomography (CT) colonographic data sets, and assessed its performance based on colonoscopy as the gold standard. In this scheme, a thick region encompassing the entire colonic wall is extracted from an isotropic volume reconstructed from the CT images in CT colonography. Polyp candidates are detected by first computing of 3-D geometric features that characterize polyps, folds, and colonic walls at each voxel in the extracted colon, and then segmenting of connected components corresponding to suspicious regions by hysteresis thresholding based on these geometric features. We apply fuzzy clustering to these connected components to obtain the polyp candidates. False-positive (FP) detections are then reduced by computation of several 3-D volumetric features characterizing the internal structures of the polyp candidates, followed by the application of discriminant analysis to the feature space generated by these volumetric features. The locations of the polyps detected by our computerized method were compared to the gold standard of conventional colonoscopy. The performance was evaluated based on 43 clinical cases, including 12 polyps determined by colonoscopy. Our computerized scheme was shown to have the potential to detect polyps in CT colonography with a clinically acceptable high sensitivity and a low FP rate.
Associations between Estrogen Receptor–Negative Breast Cancer and Timing of Reproductive Events Differ between African American and European American Women

The effects of reproductive factors on breast cancer risk seem to differ by estrogen receptor (ER) status. Menarche and first live birth (FLB) tend to occur at younger ages in African Americans (AA) than European Americans (EA), and could play a role in breast cancer disparities. In the Women's Circle of Health Study, a case–control study of breast cancer in EA and AA women, in-person interviews were conducted to collect epidemiologic data, including reproductive histories. Data on ER status, abstracted from pathology reports, were available for 814 AA and 538 EA breast cancer cases, and were analyzed with 1015 AA and 715 EA controls, to evaluate associations between subgroups and age at menarche, age at FLB, and the interval between those ages. Among AA women, later age at menarche (≥14 years) was associated with reduced risk of both ER+ and ER− breast cancer, with ORs strongest for ER− disease [OR = 0.57; 95% confidence interval (CI), 0.37–0.88]; associations were weaker and nonsignificant for EA women. There were no significant associations with age at FLB, but AA women with a FLB within 15 years of menarche had increased risk of ER− disease (OR = 2.26; 95% CI, 1.29–3.95), with no significant associations among EAs. In our data, earlier age at menarche and shorter intervals until FLB are associated with ER− breast cancer in AA women; differential distributions by race of these and other reproductive risk factors could contribute to the higher prevalence of ER− breast cancer in AA women. Cancer Epidemiol Biomarkers Prev; 23(6); 1115–20. ©2014 AACR.
Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) based on plastid-encoded RuBisCo spacer and nuclear-encoded ITS sequence comparisons.

Concatenated sequences from the plastid-encoded RuBisCo spacer and nuclear-encoded rDNA ITS region of the Alariaceae, Laminariaceae, and Lessoniaceae as currently recognized were used to determine the phylogeny of kelps (Phaeophyceae). Our analyses indicate that all taxa in the Alariaceae, Laminariaceae, and Lessoniaceae form a monophyletic lineage (the Laminariales sensu stricto). The phylogenetic analyses show that the kelps form eight well-supported clades (represented by Egregia, Laminaria, Hedophyllum, Macrocystis, Alaria, Agarum, Ecklonia, and Lessonia) that conform to the tribes of the current morphological classification system of the "advanced" kelps. Our results suggest that the kelps should be classified into eight families rather than the three that are presently used. The interrelationships among the eight lineages were, however, unresolved in the phylogenetic analyses. In all trees, Egregia diverged first and is the sister to the other kelp taxa. Our phylogenetic analyses also indicate that Kjellmaniella and Laminaria do not form a monophyletic group. Taken together, the RuBisCo spacer and rDNA ITS prove useful for understanding the evolutionary history of the advanced kelps and provide a new framework for establishing the systematics of these commercially important brown algae.
Muscle activation during low-intensity muscle contractions with restricted blood flow

Abstract We examined muscle activation during low-intensity muscle contractions with a moderate restriction of blood flow and complete occlusion of blood flow. Unilateral elbow flexion muscle contractions (20% of 1-RM) were performed in Experiment 1 (30 contractions), Experiment 2 (3 sets × 10 contractions), and Experiment 3 (30 repetitive contractions followed by 3 sets × 15 contractions) with moderate restriction, complete occlusion of blood flow or unrestricted blood flow (control). Electromyography (EMG) was recorded from surface electrodes placed on the biceps brachii muscle and the integrated EMG (iEMG) and mean power frequency (MPF) obtained. During Experiments 1 and 2, muscle activation was progressively increased in complete occlusion and moderate restriction of blood flow to levels greater than in the control. The decline in maximal voluntary isometric contraction (MVC) following the bout of contractions was greater with complete occlusion (39–48%) than moderate restriction of blood flow (16–19%); control MVC did not change. In Experiment 3, changes in MVC, iEMG, and MPF were greater with moderate restriction of blood flow than in the control but comparable with complete occlusion of blood flow where less total work was performed. In conclusion, moderate restriction of blood flow results in similar neural manifestations in muscle as complete occlusion of blood flow but without the apparent contractile/metabolic impairment observed with complete occlusion. Thus, low-intensity muscle contractions, with moderate restriction of blood flow, leads to more intense activation of the muscle relative to the external load.