Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving disulfide connectivity prediction with sequential distance between oxidized cysteines

SUMMARY Predicting disulfide connectivity precisely helps towards the solution of protein structure prediction. In this study, a descriptor derived from the sequential distance between oxidized cysteines (denoted as DOC) is proposed. An approach using support vector machine (SVM) method based on weighted graph matching was further developed to predict the disulfide connectivity pattern in proteins. When DOC was applied, prediction accuracy of 63% for our SVM models could be achieved, which is significantly higher than those obtained from previous approaches. The results show that using the non-local descriptor DOC coupled with local sequence profiles significantly improves the prediction accuracy. These improvements demonstrate that DOC, with a proper scaling scheme, is an effective feature for the prediction of disulfide connectivity. The method developed in this work is available at the web server PreCys (prediction of cys-cys linkages of proteins).
A computational technique for evaluating and propagating the uncertainty of complex-valued quantities

This paper builds on recent contributions to ARFTG on the calculation and propagation of measurement uncertainty for complex-valued quantities according to N.M. Ridler and M.J. Salter (2000) and N.M. Ridler and M.J. Salter (2001). It describes the design of a simple software framework that substantially reduces the complexity of uncertainty calculations, while adhering to international best practice. The design is novel in several respects. It implicitly obtains the necessary partial derivatives (sensitivity coefficients) and has an internal structure that is hierarchical and modular. It can provide support for dynamic modularity (plug-and-play) and could be used in complex instrumentation systems to provide full low-level support for calculations that can propagate uncertainty.
The Collagenolytic Activity of Cathepsin K Is Unique among Mammalian Proteinases*

Type I collagen fibers account for 90% of the organic matrix of bone. The degradation of this collagen is a major event during bone resorption, but its mechanism is unknown. A series of data obtained in biological models strongly suggests that the recently discovered cysteine proteinase cathepsin K plays a key role in bone resorption. Little is known, however, about the actual action of cathepsin K on type I collagen. Here, we show that the activity of cathepsin K alone is sufficient to dissolve completely insoluble collagen of adult human cortical bone. We found that the collagenolytic activity of cathepsin K is directed both outside the helical region of the molecule, i.e. the typical activity of cysteine proteinases, and at various sites inside the helical region, hitherto believed to resist all mammalian proteinases but the collagenases of the matrix metalloproteinase family and the neutrophil elastase. This property of cathepsin K is unique among mammalian proteinases and is reminiscent of bacterial collagenases. It is likely to be responsible for the key role of cathepsin K in bone resorption.
Discovering value from community activity on focused question answering sites: a case study of stack overflow

Question answering (Q&A) websites are now large repositories of valuable knowledge. While most Q&A sites were initially aimed at providing useful answers to the question asker, there has been a marked shift towards question answering as a community-driven knowledge creation process whose end product can be of enduring value to a broad audience. As part of this shift, specific expertise and deep knowledge of the subject at hand have become increasingly important, and many Q&A sites employ voting and reputation mechanisms as centerpieces of their design to help users identify the trustworthiness and accuracy of the content. To better understand this shift in focus from one-off answers to a group knowledge-creation process, we consider a question together with its entire set of corresponding answers as our fundamental unit of analysis, in contrast with the focus on individual question-answer pairs that characterized previous work. Our investigation considers the dynamics of the community activity that shapes the set of answers, both how answers and voters arrive over time and how this influences the eventual outcome. For example, we observe significant assortativity in the reputations of co-answerers, relationships between reputation and answer speed, and that the probability of an answer being chosen as the best one strongly depends on temporal characteristics of answer arrivals. We then show that our understanding of such properties is naturally applicable to predicting several important quantities, including the long-term value of the question and its answers, as well as whether a question requires a better answer. Finally, we discuss the implications of these results for the design of Q&A sites.
Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm[W]

This work uses deep sequencing of RNAs from maize endosperm and embryo to identify 54 maternally expressed genes and 46 paternally expressed genes and then examines genome-wide DNA methylation and gene expression, finding hypomethylation of the maternal allele and endosperm-specific expression for many of the imprinted genes. Imprinting describes the differential expression of alleles based on their parent of origin. Deep sequencing of RNAs from maize (Zea mays) endosperm and embryo tissue 14 d after pollination was used to identify imprinted genes among a set of ~12,000 genes that were expressed and contained sequence polymorphisms between the B73 and Mo17 genotypes. The analysis of parent-of-origin patterns of expression resulted in the identification of 100 putative imprinted genes in maize endosperm, including 54 maternally expressed genes (MEGs) and 46 paternally expressed genes (PEGs). Three of these genes have been previously identified as imprinted, while the remaining 97 genes represent novel imprinted maize genes. A genome-wide analysis of DNA methylation identified regions with reduced endosperm DNA methylation in, or near, 19 of the 100 imprinted genes. The reduced levels of DNA methylation in endosperm are caused by hypomethylation of the maternal allele for both MEGs and PEGs in all cases tested. Many of the imprinted genes with reduced DNA methylation levels also show endosperm-specific expression patterns. The imprinted maize genes were compared with imprinted genes identified in genome-wide screens of rice (Oryza sativa) and Arabidopsis thaliana, and at least 10 examples of conserved imprinting between maize and each of the other species were identified.
Unsupervised estimation of segmentation quality using nonnegative factorization

We propose an unsupervised method for evaluating image segmentation. Common methods are typically based on evaluating smoothness within segments and contrast between them, and the measure they provide is not explicitly related to segmentation errors. The proposed approach differs from these methods on several important points and has several advantages over them. First, it provides a meaningful, quantitative assessment of segmentation quality, in precision/recall terms, which were applicable so far only for supervised evaluation. Second, it builds on a new image model, which characterizes the segments as a mixture of basic feature distributions. The precision/recall estimates are then obtained by a nonnegative matrix factorization (NMF) process. A third important advantage is that the estimates, which are based on intrinsic properties of the specific image being evaluated and not on a comparison to typical images (learning), are relatively robust to context factors such as image quality or the presence of texture. Experimental results demonstrate the accuracy of the precision/recall estimates in comparison to ground truth based on human judgment. Moreover, it is shown that tuning a segmentation algorithm using the unsupervised measure improves the algorithm's quality (as measured by a supervised method).
THE DENSEST LATTICE PACKING OF TETRAHEDRA

The problem of finding the densest packing of tetrahedra was first suggested by Hubert [3, p. 319]. Minkowski [4] attempted to find the densest lattice packing of tetrahedra, but his result is invalid due to the incorrect assumption that the difference body of a regular tetrahedron was a regular octahedron. A lower bound for the maximum density of such a packing has been given by Groemer [ l ] as 18/49. The purpose of this paper is to announce the proof that 18/49 is in fact the maximum possible density. We shall use the term convex body to mean any compact, convex set in three dimensions with nonempty interior, and lattice to mean the collection of all points (vectors) mA+nB+pC, where m, n, p range over all integers and A, B, C are three fixed linearly independent vectors. If J is a convex body and A is a lattice such that, when x and y are distinct points of A, the bodies x + J and y + J have no interior points in common, then the collection of bodies A + J = {x + J : x £ A } is said to form a lattice packing. If A(A) = |det(^4, Bf C)\, and Vol(J) represents the volume of J , then the density of the packing is defined to be Vol(J)/A(A). Minkowski [4] showed that A + J is a lattice packing if and only if there are no points of A other than the origin in the interior of the difference body J —J = {x— y:x, yÇzJ}When the latter condition holds, A is said to be admissible for the difference body. A lattice is critical for a difference body if it is admissible and if no other admissible lattice has a smaller determinant. I t follows that the problem of finding the densest lattice packing for a given convex body J is equivalent to that of finding a critical lattice for J—J. The following lemmas are also from Minkowski's paper.
Comparison of Three Methods for Measuring Intracompartmental Pressure in Injured Limbs of Trauma Patients

Objectives: To compare three commonly used methods and devices developed for measurement of intracompartmental pressure in injured limbs. Setting: Level II regional trauma center. Patients/Participants: Consecutive patients treated for extremity trauma suspected to have compartment syndrome. Intervention: Analysis of compartment pressure data collected using 1) a solid-state transducer intracompartmental catheter; 2) an electronic transducer-tipped catheter; and 3) a modification of Whitesides' needle manometer technique using a straight 18-gauge needle, arterial line transducer, and central venous pressure monitor. All measurements were performed in random order within an area 1.5 cm in diameter. Main Outcome Measurements: Statistical analysis evaluating differences in measured data between methods and whether choice of method might alter treatment. Results: Intracompartmental pressure was measured by each method in 97 muscle compartments in 31 injured limbs of 26 trauma patients suspected to have a compartment syndrome. The overall intraclass correlation coefficient for the three methods was 0.83 (range, 0.77-0.88), indicating only satisfactory agreement among the methods. The mean difference among measurements in each compartment was 8.3 mm Hg (range, 0-51 mm Hg), including 81 (27%) major differences exceeding 10 mm Hg and 72 (24%) minor differences of 6 to 10 mm Hg. Conclusions: The methods were similar but not completely reliable for measuring intracompartmental pressure in trauma patients. Although all methods appeared useful as aids in diagnosis of compartment syndrome, intracompartmental pressure data, especially single readings, must be interpreted in view of clinical findings.
Assumed similarity between self and other: Effect of expectation of future interaction with that other.

This experiment examined the effect of expecting to interact socially with another person upon the degree of attitudinal similarity assumed to exist between oneself and that person. Male and female undergraduates were tested individually along with a same-sex undergraduate confederate who posed as a naive subject. The subject and confederate independently examined a written account of factual evidence ostensibly presented during an actual courtroom trial and independently indicated how likely they would be to render a verdict of guilty. They also indicated their own opinions on four issues irrelevant to the court case. As hypothesized, subjects projected their own likely-to-vote-guilty response onto the confederate to a much greater degree when they expected to discuss the court case to agreement with that other than when they did not. Projection of similarity on the issues irrelevant to the case was not appreciably influenced by the expectation manipulation. The results argue that assumed similarity judgments are not entirely attributable to an availability heuristic. Instead, such judgments seem to have a functional value for the perceiver.
An examination of the mutual impact of students' sense of school belonging and adjustment in a sample of urban, ethnic-minority, elementary-aged students

OF THE DISSERTATION An Examination of the Mutual Impact of Students’ Sense of School Belonging and Adjustment in a Sample of Urban, Ethnic-minority, Elementary-aged students by LINDA A. CEDENO Dissertation Director: Maurice J. Elias, Ph.D. The purpose of this study was to investigate the reciprocal relationship between students’ sense of school belonging, and their behavioral and psychological adjustment during one academic year in a sample of urban, low-income, African American and Latino, elementary-aged students. Data from 410 2 nd and 5 th grade students were used in the analyses, drawn from twenty-three classes, spanning seven elementary schools. Students completed self-reports of perceived sense of school belonging and self-concept during the Fall and Spring semesters of one academic year. For the corresponding year, teachers completed a teacher-rated survey assessing social skills, problem behaviors, and academic competence for each student in their classes in the Fall and Spring. Results indicated that females reported higher levels of school belonging than their male counterparts; differential effects by ethnicity or age were not observed. Students’ sense of school belonging was positively correlated with social skills, self-concept, and academic competence; and inversely correlated with problem behaviors. Overall levels of school belonging did not differ between the Fall and Spring. Reported levels of school belonging in the Fall predicted problem behaviors in the Spring controlling for previous levels, though, Fall levels of school belonging were not associated with teacher-rated
Adverse Event Burden, Resource Use, and Costs Associated with Immunosuppressant Medications for the Treatment of Systemic Lupus Erythematosus: A Systematic Literature Review

This paper assessed the burden of adverse events (AEs) associated with azathioprine (AZA), cyclophosphamide (CYC), mycophenolate mofetil (MMF), methotrexate (MTX), and cyclosporine (CsA) in patients with systemic lupus erythematosus (SLE). Thirty-eight publications were included. Incidence of AEs ranged from 42.8% to 97.3%. Common AEs included infections (2.4–77%), gastrointestinal AEs (3.2–66.7%), and amenorrhea and/or ovarian complications (0–71%). More hematological cytopenias were associated with AZA (14 episodes) than MMF (2 episodes). CYC was associated with more infections than MMF (40–77% versus 12.5–32%, resp.) or AZA (17–77% versus 11–29%, resp.). Rates of hospitalized infections were similar between MMF and AZA patients, but higher for those taking CYC. There were more gynecological toxicities with CYC than MMF (32–36% versus 3.6–6%, resp.) or AZA (32–71% versus 8–18%, resp.). Discontinuation rates due to AEs were 0–44.4% across these medications. In summary, the incidence of AEs associated with SLE immunosuppressants was consistently high as reported in the literature; discontinuations due to these AEs were similar across treatments. Studies on the economic impact of these AEs were sparse and warrant further study. This paper highlights the need for more treatment options with better safety profiles.
Long‐range cortical dynamics: a perspective from the mouse sensorimotor whisker system

In the mammalian neocortex, the capacity to dynamically route and coordinate the exchange of information between areas is a critical feature of cognitive function, enabling processes such as higher‐level sensory processing and sensorimotor integration. Despite the importance attributed to long‐range connections between cortical areas, their exact operations and role in cortical function remain an open question. In recent years, progress has been made in understanding long‐range cortical circuits through work focused on the mouse sensorimotor whisker system. In this review, we examine recent studies dissecting long‐range circuits involved in whisker sensorimotor processing as an entry point for understanding the rules that govern long‐range cortical circuit function.
Behavioral and transcriptional patterns of protracted opioid self‐administration in mice

Chronic exposure to opioids induces adaptations in brain function that lead to the formation of the behavioral and physiological symptoms of drug dependence and addiction. Animal models commonly used to test these symptoms typically last less than two weeks, which is presumably too short to observe the alterations in the brain that accompany drug addiction. Here, we analyzed the phenotypic and molecular effects of nearly lifelong morphine or saccharin intake in C57BL/6J mice. We used multiple paradigms to evaluate the symptoms of compulsive drug intake: a progressive ratio schedule, intermittent access and a schedule involving a risk of punishment were programmed into an automated IntelliCage system. Gene expression profiles were evaluated in the striatum using whole‐genome microarrays and further validated using quantitative polymerase chain reaction in the striatum and the prefrontal cortex. Mice voluntary self‐administering morphine showed addiction‐related behavioral pattern that included: higher motivation to work for a drug reward, increased reward seeking and increased craving. The analysis of molecular changes revealed a tolerance effect in the transcriptional response to morphine injection (20 mg/kg, ip), as well as some long‐lasting alterations in gene expression profiles between the analyzed groups of animals. Interestingly, among the morphine‐drinking animals, certain transcriptional profiles were found to be associated with alterations in behavior. In conclusion, our model represents a novel approach for investigating the behavioral and molecular mechanisms underlying opioid addiction. Prolonged morphine intake caused adaptive processes in the brain that manifested as altered behavior and transcriptional sensitivity to opioids.
Multilabel Subject-Based Classification of Poetry

Oftentimes, the question "what is this poem about? " has no trivial answer, regardless of length, style, author, or context in which the poem is found. We propose a simple system of multi-label classification of poems based on their subjects following the categories and subcategories as laid out by the Poetry Foundation. We make use of a model that combines the methodologies of tf-idf and Latent Dirichlet Allocation for feature extraction, and a Support Vector Machine model for the classification task. We determine how likely it is for our models to correctly classify each poem they read into one or more main categories and subcategories. Our contribution is, thus, a new method to automatically classify poetry given a set and various subsets of categories.
Online Deception Investigation: Content Analysis and Cross-Cultural Comparison

The increased use of emerging digital platforms as new tools in communication has become an integral part of business activities and the social lives of many individuals. Given the Internet’s vulnerable design, however, the rapid growth of online deception poses an extremely serious problem, and there is still little scholarly work on this issue. Using online deception cases from Taiwan, the authors undertook the current study with a twofold objective: (1) to investigate the distribution and patterns of deception tactics, and (2) to test hypotheses about how the identity of a potential victim and the purported identity of the deceiver affect the selection of a specific deception tactic. They found that the selection of deception tactics is significantly influenced by the characteristics of the deceivers and their targets. Implications of their results are also discussed.
[Clinical significance of HER-2/neu expression in colon cancer].

BACKGROUND/AIMS The HER-2/neu protein is involved in normal cell proliferation and tissue growth because it is extensively homologous and related to epidermal growth factor receptor. As a prognostic marker, HER-2/neu is used to forecast the clinical course and poor outcome in breast cancer. As a predictive marker, HER-2/neu is used to predict the therapeutic response to adjuvant chemotherapy and endocrine therapy in breast cancer. In this study, we investigated the relationships between clinical and pathologic characteristics of tumor and prognosis according to the HER-2/neu expression in colon cancer. This study was conducted for the future introduction of Herceptin therapy for colon cancer patients. METHODS Overexpression of HER-2/neu was examined by semiquantitative standardized immunohistochemical staining kit in 88 patients with colon cancer. The patients underwent curative surgery at the Kangbuk Samsung Hospital. RESULTS Overexpression of HER-2/neu was detected in 11 (12.5%) of 88 patients. Tumors with positive HER-2/neu staining showed a tendency for higher rates of nodal metastasis and poor mean survival (1,646 +/- 269 vs 2,631 +/- 141 days) and 5-year survival (65.5% vs 78.9%). CONCLUSIONS Tumors with positive HER-2/neu staining showed a tendency for higher rates for nodal metastasis and poor clinical survival rate.
Mapping global fisheries: sharpening our focus

Mapping global landings is an important prerequisite for examining causal relationships between fishing and ecological change. Landing statistics, typically provided with poor spatial precision, can be disaggregated into a grid system of spatial cells (30 min ·30 min) using a rule-based approach and ancillary data about distributions of fished taxa and fishing access of reporting countries. Presentation of time series catch composition is then possible for many types of marine areas including biogeochemical provinces, large marine ecosystems and exclusive economic zones.
Vitamin D status in Chinese pregnant women and their newborns in Beijing and their relationships to birth size

Abstract Objective To evaluate the prevalence of vitamin D deficiency in pregnant women and their newborns in Beijing, China and the influence of vitamin D deficiency on birth size. Design A cross-sectional study. Setting Data were collected from pregnant women who delivered during April to May 2010 at 306 Hospital of PLA in Beijing, China. Subjects Participants in the study were seventy healthy nulliparous pregnant women with singleton pregnancies who delivered healthy babies at full term and their newborns. Results Severe vitamin D deficiency (25-hydroxyvitamin D (25(OH)D) < 25 nmol/l) was detected in 54·5 % of mothers and 46·6 % of newborns. Neither mothers nor newborns had serum 25(OH)D concentrations that reached the normal level (>75 nmol/l). The concentration of 25(OH)D in mothers was positively correlated with that in cord blood (r = 0·89, P < 0·001). Newborns of mothers with severe vitamin D deficiency had lower birth length and birth weight. The head circumference and birth weight were lower in vitamin D-deficient newborns. Conclusions The study indicates that pregnant women and neonates residing in Beijing are at high risk of vitamin D deficiency. Neonatal 25(OH)D concentrations are dependently related to maternal 25(OH)D levels. Maternal and neonatal vitamin D status influences newborn size.