Miracle-dz/UniFAR-FTUs huggingface dataset:
FAST: A novel protein structure alignment algorithm

We present a novel algorithm named FAST for aligning protein three‐dimensional structures. FAST uses a directionality‐based scoring scheme to compare the intra‐molecular residue–residue relationships in two structures. It employs an elimination heuristic to promote sparseness in the residue‐pair graph and facilitate the detection of the global optimum. In order to test the overall accuracy of FAST, we determined its sensitivity and specificity with the SCOP classification (version 1.61) as the gold standard. FAST achieved higher sensitivities than several existing methods (DaliLite, CE, and K2) at all specificity levels. We also tested FAST against 1033 manually curated alignments in the HOMSTRAD database. The overall agreement was 96%. Close inspection of examples from broad structural classes indicated the high quality of FAST alignments. Moreover, FAST is an order of magnitude faster than other algorithms that attempt to establish residue–residue correspondence. Typical pairwise alignments take FAST less than a second with a Pentium III 1.2GHz CPU. FAST software and a web server are available at http://biowulf.bu. edu/FAST/. Proteins 2005. © 2004 Wiley‐Liss, Inc.
The Research and Simulation Realization of PoC Service Based on TD-SCDMA Network

In view of the development of the Push to talk over Cellular (PoC), this paper proposes two different network schemes, and every network unit function is introduced. Then the communication performance is simulated about the two schemes. Lastly, the communications of the PoC service based on TD-SCDMA network is simulated by computer. By simulation we know it is able to realize the PoC service based on TD-SCDMA network and the correlative communications parameters are analyzed. So, the existing problem of PoC service based on TD network is discussed, and the idea of the development in the next step is proposed.
Mechanical restraint of adult psychiatric inpatients: a literature review

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An ATP Binding Cassette Transporter Is Required for Cuticular Wax Deposition and Desiccation Tolerance in the Moss Physcomitrella patens[W]

This study reveals that the moss Physcomitrella patens has a cuticle that is compositionally and structurally similar to those of later diverging land plants. A genetic knockout of a moss putative ABCG transporter, ABCG7, is deficient in cuticular wax accumulation and susceptible to desiccation stress. The cuticle appears to be a highly conserved evolutionary adaptation to life on land. The plant cuticle is thought to be a critical evolutionary adaptation that allowed the first plants to colonize land, because of its key roles in regulating plant water status and providing protection from biotic and abiotic stresses. Much has been learned about cuticle composition and structure through genetic and biochemical studies of angiosperms, as well as underlying genetic pathways, but little is known about the cuticles of early diverging plant lineages. Here, we demonstrate that the moss Physcomitrella patens, an extant relative of the earliest terrestrial plants, has a cuticle that is analogous in both structure and chemical composition to those of angiosperms. To test whether the underlying cuticle biosynthetic pathways were also shared among distant plant lineages, we generated a genetic knockout of the moss ATP binding cassette subfamily G (ABCG) transporter Pp-ABCG7, a putative ortholog of Arabidopsis thaliana ABCG transporters involved in cuticle precursor trafficking. We show that this mutant is severely deficient in cuticular wax accumulation and has a reduced tolerance of desiccation stress compared with the wild type. This work provides evidence that the cuticle was an adaptive feature present in the first terrestrial plants and that the genes involved in their formation have been functionally conserved for over 450 million years.
Association of Exposure to Phthalates with Endometriosis and Uterine Leiomyomata: Findings from NHANES, 1999–2004

Background Phthalates are ubiquitous chemicals used in consumer products. Some phthalates are reproductive toxicants in experimental animals, but human data are limited. Objective We conducted a cross-sectional study of urinary phthalate metabolite concentrations in relation to self-reported history of endometriosis and uterine leiomyomata among 1,227 women 20–54 years of age from three cycles of the National Health and Nutrition Examination Survey (NHANES), 1999–2004. Methods We examined four phthalate metabolites: mono(2-ethylhexyl) phthalate (MEHP), monobutyl phthalate (MBP), monoethyl phthalate (MEP), and monobenzyl phthalate (MBzP). From the last two NHANES cycles, we also examined mono(2-ethyl-5-hydroxyhexyl) phthalate (MEHHP) and mono(2-ethyl-5-oxohexyl) phthalate (MEOHP). We used logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs), adjusting for potential confounders. Results Eighty-seven (7%) and 151 (12%) women reported diagnoses of endometriosis and leiomyomata, respectively. The ORs comparing the highest versus lowest three quartiles of urinary MBP were 1.36 (95% CI, 0.77–2.41) for endometriosis, 1.56 (95% CI, 0.93–2.61) for leiomyomata, and 1.71 (95% CI, 1.07–2.75) for both conditions combined. The corresponding ORs for MEHP were 0.44 (95% CI, 0.19–1.02) for endometriosis, 0.63 (95% CI, 0.35–1.12) for leiomyomata, and 0.59 (95% CI, 0.37–0.95) for both conditions combined. Findings for MEHHP and MEOHP agreed with findings for MEHP with respect to endometriosis only. We observed null associations for MEP and MBzP. Associations were similar when we excluded women diagnosed > 7 years before their NHANES evaluation. Conclusion The positive associations for MBP and inverse associations for MEHP in relation to endometriosis and leiomyomata warrant investigation in prospective studies.
The Environmental Impacts of Sprawl: Emergent Themes from the Past Decade of Planning Research

This article reviews studies published in English language planning journals since 2001 that focus on the environmental impacts of sprawl. We organise our analysis of the reviewed literature around: (1) the conceptualisation or measurement of sprawl; (2) a comparison of research methods employed and findings with respect to four categories of environmental impacts—air, energy, land, and water; and (3) an exploration of emergent and cross-cutting themes. We hypothesise that the trend towards breaking down silos observable in other areas of planning scholarship is also reflected in the recent sprawl literature and structure our review to test this proposition. International in scope, our work demonstrates how focusing on outcomes can facilitate balanced comparisons across geographic contexts with varying rates of urbanisation and affluence. We find that the sprawl research published in planning journals over the past decade frequently engages with broader themes of resilience and justice, increasingly considers multiple environmental outcomes, and suggests a convergence in the way sprawl is studied that transcends national boundaries as well as the developing-developed country dichotomy.
Early indicators of prognosis in fulminant hepatic failure: An assessment of the Model for End‐Stage Liver Disease (MELD) and King's College Hospital Criteria

While King's Hospital Criteria (KCH) criteria are used worldwide, the Model for End‐Stage Liver Disease (MELD) is a more recently developed scoring system that has been validated as an independent predictor of patient survival in conditions for liver transplantation (LT). The aim of the present study was to compare MELD and KCH criteria with other early clinical prognostic indicators (CPI) in a cohort of patients with fulminant hepatic failure (FHF). A total of 144 patients (mean age 31.7 ± 14.7 yr; range 12–82 yr; 62 males) with FHF due to acute viral hepatitis were included into the study. Variables found significant on univariate analysis were entered into a multivariate logistic regression analysis. A total of 52 (36.1%) patients survived, the remaining 92 (63.9%) died. Univariate analysis showed that age, duration of jaundice, jaundice‐encephalopathy interval (JEI), grade of encephalopathy, presence of cerebral edema, bilirubin, prothrombin time, creatinine, and MELD score were significantly different between survivors and nonsurvivors. Multivariate logistic regression identified 6 independent CPI of adverse outcome on admission: age ≥50 yr, JEI >7 days, grade 3 or 4 encephalopathy, presence of cerebral edema, prothrombin time ≥35 seconds, and creatinine ≥1.5 mg/dL. Presence of any 3 of 6 CPI was optimum in identifying survivors and nonsurvivors. A MELD score of ≥33 was found to be best discriminant between survivors and nonsurvivors by the construction of receiver operating characteristic (ROC) curves. Any 3 CPI were superior to MELD and KCH criteria in predicting the outcome (c‐statistic [95% confidence interval]: CPI 0.802 [0.726–0.878], MELD 0.717 [0.636–0.789], and KCH criteria 0.676 (0.588–0.764); P values: CPI vs. MELD 0.045, CPI vs. KCH criteria 0.019, and MELD vs. KCH criteria 0.472). In conclusion, MELD and KCH criteria are not as useful as a combination of other early CPI in predicting adverse outcome in patients with FHF due to acute viral hepatitis. Liver Transpl, 2007. © 2007 AASLD.
Neuropsychological Differentiation of Late-Onset Schizophrenia and Dementia of the Alzheimer's Type

Late-onset schizophrenia and dementia of the Alzheimer's type (DAT) often present with some pathological and behavioral commonalities. Specifically, both illnesses may involve varying degrees of delusional manifestation, apathy, lateral/third-ventricular enlargement, reduced frontal lobe activity, and hippocampal atrophy. Moreover, patients with either disease have shown comparable cognitive impairment on standardized neuropsychological tests. As such, a differential diagnosis of the 2 disorders on the basis of such testing can prove to be difficult. This study evaluated the neuropsychological test results of 32 patients with late-onset schizophrenia and 32 patients with DAT to distinguish the tests that best differentiate the 2 disorders. Results indicate that the Wechsler Adult Intelligence Scale-Revised Similarities subtest and the California Verbal Learning Test (both short- and long-delay free recall) correspond to sensitive diagnostic neuropsychological measures. This investigation was preliminary in nature, and should aid in the development of a definitive differential profile.
Use of an owner questionnaire to evaluate long-term surgical outcome and chronic pain after cranial cruciate ligament repair in dogs: 253 cases (2004-2006).

OBJECTIVE To evaluate, by means of an owner questionnaire, long-term outcome and prevalence of chronic pain after cranial cruciate ligament (CCL) surgery in dogs. DESIGN Retrospective case series. ANIMALS 253 dogs with surgically treated CCL rupture. PROCEDURES Data from surgical records of dogs that underwent surgical repair of CCL between 2004 and 2006 were reviewed. An owner questionnaire, including the validated Helsinki chronic pain index (HCPI), served to evaluate long-term outcome and prevalence of chronic pain after surgical repair by means of intracapsular, extracapsular, or osteotomy techniques. Additional questions inquired about recovery and rehabilitation after surgery, current well-being, medications, and adjunct treatments. RESULTS Of 507 questionnaires, 272 (53.6%) were returned; 19 were excluded because of incomplete answers. Mean ± SD follow-up time was 2.7 ± 0.8 years (range, 1.3 to 4.5 years). Owners considered surgical outcome as excellent in 122 of 226 (54.0%) dogs, good in 97 (42.9%), fair in 0 (0%), and poor in 7 (3.1%). At follow-up, the mean ± SD HCPI for 206 dogs was 8.9 ± 6.3 (range, 0 to 24). Of these 206 dogs, 64 (31.1%) had an HCPI ≥ 12, indicating chronic pain. Mean HCPI in dogs with a good outcome (11.8 ± 5.4; 95% confidence interval, 10.6 to 12.9) was significantly higher than that for dogs with an excellent outcome (6.2 ± 5.7; 95% confidence interval, 5.1 to 7.2). Owner-reported postoperative lameness was significantly shorter after osteotomy techniques, compared with lameness duration after the intracapsular technique. CONCLUSIONS AND CLINICAL RELEVANCE On the basis of owner assessment, long-term chronic pain was found in approximately 30% of dogs after CCL repair.
Effect of passive polarizing three‐dimensional displays on surgical performance for experienced laparoscopic surgeons

Although the potential benefits of stereoscopic laparoscopy have been recognized for years, the technology has not been adopted because of poor operator tolerance. Passive polarizing projection systems, which have revolutionized three‐dimensional (3D) cinema, are now being trialled in surgery. This study was designed to see whether this technology resulted in significant performance benefits for skilled laparoscopists.
Random Access Game and Medium Access Control Design

Motivated partially by a control-theoretic viewpoint, we propose a game-theoretic model, called random access game, for contention control. We characterize Nash equilibria of random access games, study their dynamics, and propose distributed algorithms (strategy evolutions) to achieve Nash equilibria. This provides a general analytical framework that is capable of modeling a large class of system-wide quality-of-service (QoS) models via the specification of per-node utility functions, in which system-wide fairness or service differentiation can be achieved in a distributed manner as long as each node executes a contention resolution algorithm that is designed to achieve the Nash equilibrium. We thus propose a novel medium access method derived from carrier sense multiple access/collision avoidance (CSMA/CA) according to distributed strategy update mechanism achieving the Nash equilibrium of random access game. We present a concrete medium access method that adapts to a continuous contention measure called conditional collision probability, stabilizes the network into a steady state that achieves optimal throughput with targeted fairness (or service differentiation), and can decouple contention control from handling failed transmissions. In addition to guiding medium access control design, the random access game model also provides an analytical framework to understand equilibrium and dynamic properties of different medium access protocols.
Stock Market Prediction Using a Hybrid Neuro-fuzzy System

Stock market prediction is an important area of financial forecasting, which is of great interest to stock investors, stock traders and applied researchers. Main issues in developing a fully automated stock market prediction system are: feature extraction from the stock market data, feature selection for highest prediction accuracy, the dimensionality reduction of the selected feature set and the accuracy and robustness of the prediction system. In this paper, an automated decision tree-adaptive neuro-fuzzy hybrid automated stock market prediction system is proposed. The proposed system uses technical analysis (traditionally used by stock traders) for feature extraction and decision tree for feature selection. Dimensionality reduction is carried out using fifteen different dimensionality reduction techniques. The dimensionality reduction technique producing the best prediction accuracy is selected to produce the reduced dataset. The reduced dataset is then applied to the adaptive neuro-fuzzy system for the next-day stock market prediction. The neuro-fuzzy system forms the stock market model adaptively, based on the features present in the reduced dataset. The proposed system is tested on the Bombay Stock Exchange sensitive index (BSE-SENSEX). The results show that the proposed hybrid system produces much higher accuracy when compared to stand-alone decision tree based system and ANFIS based system without feature selection and dimensionality reduction.
Modulation of cellular invasion by VEGF-C expression in squamous cell carcinoma of the head and neck.

OBJECTIVE To determine how vascular endothelial growth factor C (VEGF-C) affects tumor cell invasion and motility in squamous cell carcinoma of the head and neck (SCCHN). DESIGN A molecular biology study. The VEGF-C coding sequence was cloned into an expression vector and stably transfected into the SCCHN cell line SCC116 to create the SCC116-VEGFC line. RNA interference (RNAi) was used to block VEGF-C expression. An adenoviral system for expressing VEGF-C RNAi was developed and tested. SETTING An academic hospital laboratory. MAIN OUTCOME MEASURES Relative VEGF-C RNA levels were determined by real-time quantitative reverse transcriptase-polymerase chain reaction, and protein expression was evaluated by Western blot. Cellular invasion was evaluated by 24-hour semipermeable membrane transit assay. RESULTS SCC116-VEGFC cells had markedly increased expression of VEGF-C protein and RNA compared with normal SCC116 controls. SCC116-VEGFC cells produced marked increases in cellular invasion and motility compared with SCC116 cells. Blockade of VEGF-C expression by transfection of a VEGF-C RNAi expression plasmid into both SCC116 and SCC116-VEGFC cells induced a 38% decrease in SCCHN invasion and motility as tested by a semipermeable membrane invasion assay. We developed an adenoviral expression system for VEGF-C RNAi, which also induced a dose-dependent decrease in cellular invasion in the highly invasive DM12 cell line. CONCLUSIONS These studies demonstrate that intracellular VEGF-C levels modulate in vitro SCCHN motility and invasion. Further work is needed to clarify the specific receptors and signaling pathways that are involved in SCCHN motility. Molecular therapies that inhibit the VEGF-C pathway may have clinical potential in the treatment of lymphatic metastasis in SCCHN.
Simple cyst in the postmenopausal patient: detection and management.

The aims of our study were to determine the prevalence of simple ovarian cysts in asymptomatic postmenopausal patients and to investigate the natural history of these cysts by ultrasonographic follow‐up examinations. Three thousand five hundred and eighty‐five women participated in the volunteer pelvic cancer screening program. Entry criteria were as follows: postmenopausal, no clinical symptoms, and no previous gynecologic pathology. An anechoic, small cyst less than 5 cm in greatest diameter was classified as a simple ovarian cyst. A scoring system to determine malignant potential had been established previously. All simple cysts had a score of 2 or less and had a morphology typical of benign lesions. In the case of a positive finding, the patient would be seen at 3 to 6 month intervals. The decision for surgical intervention was made by a private gynecologist or patient or if an interval change was noted. One thousand seven hundred and sixty‐nine postmenopausal women (49.34% of all patients from the screening program) participated in this study. One hundred and sixteen simple cysts were found, with a prevalence of 6.6% in our population. Among those patients, 27 (23.28%) simple cysts resolved spontaneously, 69 (59.48%) have persisted, and 20 (17.24%) have been lost to follow‐up study. Eighteen women (26.09%) with persistent simple ovarian cyst underwent surgery. No malignant ovarian conditions were identified. In conclusion, simple ovarian cysts are more common in postmenopausal women than previously was thought. This condition is very unlikely to be malignant and can be followed conservatively.
Sum-Rate Analysis of Multiuser MIMO System with Zero-Forcing Transmit Beamforming

In this paper, we present the exact sum-rate analysis of the multiuser multiple-input multiple-output (MIMO) broadcast channel with zero-forcing transmit beamforming. We develop the analytical expressions of the ergodic sum-rate for two low-complexity user selection strategies for the important dual- transmit-antenna scenario. Based on the analytical results, we examine the parameter optimization problem to properly trade off between channel power gain and directional gain in term of maximizing the ergodic sum rate offered by multiuser diversity.
Lumbar plexus block: an anatomical study

The anatomy of the lumbar plexus and the various approaches used to perform lumbar plexus blockade are reviewed. A single needle technique for a posterior approach to the plexus at the L2–3 interspace is described. This technique was used bilaterally in six intact cadavers, and the extent of spread of an injected dye was documented photographically during a subsequent detailed dissection of the region. In all cases, dye was confined to the posterior part of the psoas muscle, and tracked down the nerves of the lumbar plexus. No dye was seen anterior to the psoas, around the sympathetic chain, on the sacral plexus or in the extradural or subarachnoid spaces. Further studies in patients with needle position and drug dispositon being confirmed using computerised tomography and X ray scanning were in agreement with the results observed in the cadavers. This technique represents a simple approach to the lumbar plexus which does not require needle localisation by X ray screening.
Wound healing and longevity: Lessons from long-lived αMUPA mice

Does the longevity phenotype offer an advantage in wound healing (WH)? In an attempt to answer this question, we explored skin wound healing in the long-lived transgenic αMUPA mice, a unique model of genetically extended life span. These mice spontaneously eat less, preserve their body mass, are more resistant to spontaneous and induced tumorigenesis and live longer, thus greatly mimicking the effects of caloric restriction (CR). We found that αMUPA mice showed a much slower age-related decline in the rate of WH than their wild-type counterparts (FVB/N). After full closure of the wound, gene expression in the skin of old αMUPA mice returned close to basal levels. In contrast, old FVB/N mice still exhibited significant upregulation of genes associated with growth-promoting pathways, apoptosis and cell-cell/cell-extra cellular matrix interaction, indicating an ongoing tissue remodeling or an inability to properly shut down the repair process. It appears that the CR-like longevity phenotype is associated with more balanced and efficient WH mechanisms in old age, which could ensure a long-term survival advantage.