Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural analysis of protein‐ligand interactions: the binding of endogenous compounds and of synthetic drugs

The large number of macromolecular structures deposited with the Protein Data Bank (PDB) describing complexes between proteins and either physiological compounds or synthetic drugs made it possible a systematic analysis of the interactions occurring between proteins and their ligands. In this work, the binding pockets of about 4000 PDB protein‐ligand complexes were investigated and amino acid and interaction types were analyzed. The residues observed with lowest frequency in protein sequences, Trp, His, Met, Tyr, and Phe, turned out to be the most abundant in binding pockets. Significant differences between drug‐like and physiological compounds were found. On average, physiological compounds establish with respect to drugs about twice as many hydrogen bonds with protein atoms, whereas drugs rely more on hydrophobic interactions to establish target selectivity. The large number of PDB structures describing homologous proteins in complex with the same ligand made it possible to analyze the conservation of binding pocket residues among homologous protein structures bound to the same ligand, showing that Gly, Glu, Arg, Asp, His, and Thr are more conserved than other amino acids. Also in the cases in which the same ligand is bound to unrelated proteins, the binding pockets showed significant conservation in the residue types. In this case, the probability of co‐occurrence of the same amino acid type in the binding pockets could be up to thirteen times higher than that expected on a random basis. The trends identified in this study may provide an useful guideline in the process of drug design and lead optimization. Copyright © 2014 John Wiley & Sons, Ltd.
Skeletal Surveys in Children With Burns Caused by Child Abuse

Objective: To determine the frequency of occult fractures in children with suspicious burns compared with children with other types of physical abuse. Methods: Child abuse outpatient clinic reports and inpatient consultations from a midwest urban children's hospital for 1989 to 2000 were reviewed. Demographic and clinical data were abstracted for patients seen because of suspected physical abuse. Patients were classified based on reason seen (burns vs other physical injuries), whether they were diagnosed as abused, and whether they had at least 1 skeletal survey. Positive skeletal surveys were defined as having a fracture that was unexplained, highly specific for abuse, or with a perpetrator confession. Results: Of 335 patients evaluated, the mean age (±SD) was 1.5 ± 1.9 years, 63% were boys, 64% were white, and 80% had skeletal surveys performed. Reasons for evaluation included 69 (21%) for burns and 266 (79%) for other injuries. After excluding patients without a final diagnosis of abuse and those presenting with obvious fractures, 5 (14%) of 36 burn patients had positive skeletal surveys compared with 45 (34%) of 133 with nonburn injuries (P = 0.02). Burn patients were older compared with those with nonburn injuries (mean ages, 1.8 ± 1.5 vs. 1.1 ± 1.6 years; P = 0.03) and were more likely to be nonwhite (69% vs. 32%; P < 0.001). Conclusions: Although young children with abusive burns have fewer occult fractures compared with those with other abusive injuries, the frequency of occult fractures is still high enough to warrant the consideration of skeletal surveys in these cases.
Challenging behaviour in Phelan-McDermid Syndrome

To date, no research has examined the presence of challenging behaviour in Phelan McDermid syndrome (PMS). In this paper, study one adopts a questionnaire methodology to delineate the prevalence and aetiology of challenging behaviour in thirty participants with PMS. Study two adopts an interview methodology to examine the form, frequency, severity and function of this behaviour in eighteen participants. Responses to the Challenging Behaviour Questionnaire indicated that, thirteen (43.3%) participants with PMS showed self-injurious behaviour, thirteen (43.3%) showed physical aggression, and twenty (66.7%) showed destruction of property. Examination of associated characteristics indicated that self-injury was associated with impulsivity; aggression was associated with younger age and compulsive behaviour; and destruction of property was associated with impulsivity and stereotyped behaviour. In study two, responses to the Challenging Behaviour Interview highlighted multiple topographies of challenging behaviour. The behaviour of most concern typically occurred every fifteen minutes. Examination of behavioural function showed that self-stimulation was the predominant function for self-injury and destruction of property. However, many behaviours were found to serve multiple functions. The results of this paper emphasise the importance of building causal models of challenging behavior that incorporates both person characteristics and environmental factors. Limitations and areas for future research are discussed.
Prediction of gestational diabetes mellitus in the first trimester: comparison of maternal fetuin-A, N-terminal proatrial natriuretic peptide, high-sensitivity C-reactive protein, and fasting glucose levels

ABSTRACT Objective We investigated the utility of maternal fetuin-A, N-terminal proatrial natriuretic peptide (pro-ANP), high-sensitivity C-reactive protein (hs-CRP), and fasting glucose levels at 11-14 gestation weeks for predicting pregnancies complicated by gestational diabetes mellitus (GDM). Subjects and methods This prospective cohort study included 327 low-risk pregnant women who completed antenatal follow-up at a tertiary research hospital between January and April 2014. Maternal blood samples were collected between 11–14 gestational weeks in the first trimester of pregnancy and then stored at –80 °C until further analyses. During follow-up, 29 (8.8%) women developed GDM. The study population was compared 1:2 with age- and body mass index-matched pregnant women who did not develop GDM (n = 59). Fasting plasma glucose (FPG) levels and serum fetuin-A, pro-ANP, and hs-CRP levels were measured using automated immunoassay systems. Results There was a significant negative correlation between fetuin-A and hs-CRP (CC = –0.21, p = 0.047) and a positive correlation between FPG and hs-CRP (CC = 0.251, p = 0.018). The areas under the receiver operating characteristic curve for diagnosing GDM were 0.337 (p = 0.013), 0.702 (p = 0.002), and 0.738 (p < 0.001) for fetuin-A, hs-CRP, and FPG, respectively. The optimal cut-off values were > 4.65, < 166, and > 88.5 mg/dL for maternal hs-CRP, fetuin-A, and FPG, respectively. Conclusion Reduced fetuin-A, elevated hs-CRP, and FPG levels in women in the first trimester can be used for the early detection of GDM. Further research is needed before accepting these biomarkers as valid screening tests for GDM.
A thymidylate synthase ternary complex-specific antibody, FTS, permits functional monitoring of fluoropyrimidines dosing

5-Fluorouracil (5FU) and similar fluoropyrimidines induce covalent modification of thymidylate synthase (TS) and inhibit its activity. They are often used to treat solid cancers, but drug resistance and toxicity are drawbacks. Therefore, there is an unmet need for a functional assay to quantify fluorouracil activity in tissues, so as to individually tailor dosing. It is cumbersome to separately quantify unmodified and 5FU-modified TS using currently available commercial anti-TS antibodies because they recognize both forms. We report here the first monoclonal antibody (FTS) specific to 5FU-modified TS. By immunoblot assay, the FTS antibody specifically recognizes modified TS in a dose-dependent manner in 5FU-treated cells, in cancer xenograft tissues of 5FU-treated mice, and in the murine tissues. In the same assay, the antibody is nonreactive with unmodified TS in untreated or treated cells and tissues. Speculatively, a high-throughput assay could be enabled by pairing anti-TS antibodies of two specificities, one recognizing only modified TS and another recognizing both forms, to structurally quantify the TS-inhibiting effect of fluorouracil at a cellular or tissue level without requiring prior protein separation. Such a development might aid preclinical analytic studies or make practical the individual tailoring of dosing.
A new concept of the anatomy of the anal sphincter mechanism and the physiology of defecation. The external anal sphincter: a triple-loop system.

Since anal sphincters are used as the continent sphincters in some urologic operations, a study of their anatomic structure and function seems necessary. The anatomy of the external anal sphincter has been studied in 18 cadavers by dissection and serial histologic sections. The muscle has been found to consist of a series of U-shaped loops which are distinguishible as three main "loops": top, intermediate, and base. The puborectalis and the deep portion of the external sphincter have been found to be one muscle which is given the name "top loop. " No concentric circular muscle bundles could be detected at any level of the external sphincter except in the base loop. A new concept of the mechanism of action of the external sphincter in anal continence and during defecation is presented. An air-tight occlusion of the anal canal could be achieved by the "triple-loop system" of the external sphincter which compresses opposed alternating anal segments. An incomplete anal occlusion by a single loop contraction is completed and potentiated by the succeeding loop action. The last fecal portion is dispelled from the anal canal by a process of "vermicular contractions" which is the result of the loop arrangement of the muscle bundles. Single-loop continence has been discussed. It is suggested that unless all three of the loops are destroyed, any single loop can act as a sphincter which maintains continence to solid stools but not to fluid ones or flatus.
Altruistic personality in the context of the empathy–altruism hypothesis

In this study the influence of the altruistic personality in general and social responsibility in particular on prosocial behaviour were investigated in the context of the empathy–altruism hypothesis. In an experiment 56 female participants had an opportunity to help a person in distress. In this setting, ease of escape without helping was manipulated. In addition, on the basis of their self‐reports of situation‐specific emotions, participants were divided into an empathic‐concern and a personal‐distress group. The results of the 2 (ease of escape) × 2 (predominant emotional response) design were in agreement with the empathy–altruism hypothesis. Further results indicated that in the easy‐escape condition an altruistic motivation prevailed, whereas in the difficult‐escape condition an egoistic motivation was more dominant. Besides the full scale, two subscales of social responsibility were formed: Moral Fulfilment of the Justified Expectations of Others and Adherence to Social Prescriptions. The full social responsibility scale was significantly related to helpfulness only in the difficult‐escape condition. Further analyses including the subscales showed that the component Moral Fulfilment of the Justified Expectations of Others correlated positively with helping in the easy‐escape condition. Results were interpreted as showing that specific profiles of personality variables are associated with helpfulness in the easy‐escape and difficult‐escape conditions. Copyright © 2004 John Wiley & Sons, Ltd.
Comparing the effectiveness of electronic diary and UX curve methods in multi-component product study

Due to the complex nature of multi-component products, methods for their user experience (UX) evaluation are critical. In this study, we evaluated the long-term UX of a multi-component product from the sports domain. We present a comparison of two remote UX evaluation methods: a weekly filled-in electronic diary and the UX Curve method for retrospective evaluation. The cost-effectiveness of the methods was evaluated using two factors: the amount of time required by 1) the researchers in employing the methods and 2) the participants to report their experiences with the method. Also, to determine the quality of the reported experiences, their content was compared between the methods. The results show that the electronic diary was more effective in revealing the experiences related to utility, missing functionalities, technical faults, dissatisfaction, and effectiveness. However, the UX Curve method was more effective in capturing the experiences related to stimulation.
A Deep Convolutional Neural Network for Background Subtraction

In this work, we present a novel background subtraction system that uses a deep Convolutional Neural Network (CNN) to perform the segmentation. With this approach, feature engineering and parameter tuning become unnecessary since the network parameters can be learned from data by training a single CNN that can handle various video scenes. Additionally, we propose a new approach to estimate background model from video. For the training of the CNN, we employed randomly 5 percent video frames and their ground truth segmentations taken from the Change Detection challenge 2014(CDnet 2014). We also utilized spatial-median filtering as the post-processing of the network outputs. Our method is evaluated with different data-sets, and the network outperforms the existing algorithms with respect to the average ranking over different evaluation metrics. Furthermore, due to the network architecture, our CNN is capable of real time processing.
Youth: A "New" Stage of life

the twentieth century, adolescence was rarely included as a stage in the life cycle. Early life began with infancy and was followed by a period of childhood that lasted until around puberty, which occurred several years later than it does today. After puberty, most young men and women simply entered some form of apprenticeship for the adult world. Not until 1 904, when G. Stanley Hall published his monumental work, Adolescence: Its Psychology and Its Relations to Physiology, Anthropology, Sociology, Sex, Crime, Religion, and Education, was this further preadult stage widely recognized. Hall's work went through many editions and was much popularized; * 'adolescence" became a household word. Hall's classic description of the sturm und drang, turbulence, ambivalence, dangers and possibilities of adolescence has since been echoed in almost every discussion of this stage of life.
Far-reaching dust distribution in galaxy discs

In most studies of dust in galaxies, dust is only detected from its emission to approximately the optical radius of the galaxy. By combining the signal of 110 spiral galaxies observed as part of the Herschel Reference Survey, we are able to improve our sensitivity by an order of magnitude over that for a single object. Here we report the direct detection of dust from its emission that extends out to at least twice the optical radius. We find that the distribution of dust is consistent with an exponential at all radii with a gradient of ∼−1.7 dex R^(−1)_(25). Our dust temperature declines linearly from ∼25 K in the centre to 15 K at R_(25) from where it remains constant out to ∼2.0 R_(25). The surface density of dust declines with radius at a similar rate to the surface density of stars but more slowly than the surface density of the star-formation rate. Studies based on dust extinction and reddening of high-redshift quasars have concluded that there are substantial amounts of dust in intergalactic space. By combining our results with the number counts and angular correlation function from the SDSS, we show that with Milky Way-type dust we can explain the reddening of the quasars by the dust within galactic discs alone. Given the uncertainties in the properties of any intergalactic dust, we cannot rule out its existence, but our results show that statistical investigations of the dust in galactic haloes that use the reddening of high-redshift objects must take account of the dust in galactic discs.
Forensic Taphonomy: The Postmortem Fate of Human Remains

Ed William D Haglund, Marcella H Sorg CRC Press, £72, pp 636 ISBN 0 849 39434 1 Rating: ! [Graphic][1] ! [Graphic][2] ! [Graphic][3] On 5 March 1940 Stalin gave the order for the NKVD to execute prisoners of war captured during the combined German and Soviet occupation of Poland. In 1943, 4500 victims were discovered in mass graves in the Katyn Forrest, after the Germans had overrun Soviet territory. The Polish government in exile demanded a commission to investigate, and an international team of forensic investigators under German authority examined the victims. This investigation placed the blame … [1]: /embed/inline-graphic-1.gif [2]: /embed/inline-graphic-2.gif [3]: /embed/inline-graphic-3.gif
Predicting Consumer's Behavior Using Eye Tracking Data

This study aimed at using eye tracking data to predict consumer's decisions. Previous research [1, 2] suggests that consumer's gaze is actively involved in preference formation. First fixation and the total fixation duration are the commonly reported measures of visual attention in consumer research. However other measures of eye tracking data like Fixation Count, Time to First Fixation have not been investigated much for their role in consumer decision. Purpose of this study was to investigate the components of eye tracking data that can predict consumer's final choices with better precision. The results suggest that fixation counts and total fixation duration predict consumer's decision to a large extent.
Transition-based Parsing with Context Enhancement and Future Reward Reranking

This paper presents a novel reranking model, future reward reranking, to re-score the actions in a transition-based parser by using a global scorer. Different to conventional reranking parsing, the model searches for the best dependency tree in all feasible trees constraining by a sequence of actions to get the future reward of the sequence. The scorer is based on a first-order graph-based parser with bidirectional LSTM, which catches different parsing view compared with the transition-based parser. Besides, since context enhancement has shown substantial improvement in the arc-stand transition-based parsing over the parsing accuracy, we implement context enhancement on an arc-eager transition-base parser with stack LSTMs, the dynamic oracle and dropout supporting and achieve further improvement. With the global scorer and context enhancement, the results show that UAS of the parser increases as much as 1.20% for English and 1.66% for Chinese, and LAS increases as much as 1.32% for English and 1.63% for Chinese. Moreover, we get state-of-the-art LASs, achieving 87.58% for Chinese and 93.37% for English.
The Role of the Supplemental Nutrition Assistance Program in the Relationship Between Food Insecurity and Probability of Maternal Depression

ABSTRACT Food insecurity is a substantial stressor for many households. Though an association between food insecurity and depression has been well established, most studies have been cross-sectional. Although many receive benefits from the Supplemental Nutrition Assistance Program (SNAP), its role in reducing distress associated with food insecurity is unclear. Using data from 1225 women who participated in the Fragile Families and Child Wellbeing Study, this study investigated whether (1) change in food security status predicts change in depression severity over a 2-year period, (2) participating in SNAP predicts depression, and (3) the relationship between food insecurity and depression varies based on receipt of SNAP. Food insecurity was linked to probability of depression over time. Additionally, for those who became food insecure over the 2-year period, losing SNAP benefits was associated with increased probability of depression, whereas gaining benefits was associated with reduced probability of depression. This suggests that the SNAP program offsets emotional hardship for those who have recently become food insecure. Further research is needed to evaluate the most efficient and efficacious means to reduce food insecurity and improve emotional well-being among vulnerable families.
On the Solution of Traveling Salesman Problems

Following the theoretical studies of J.B. Robinson and H.W. Kuhn in the late 1940s and the early 1950s, G.B. Dantzig, R. Fulk- erson, and S.M. Johnson demonstrated in 1954 that large instances of the TSP could be solved by linear programming. Their approach remains the only known tool for solving TSP instances with more than several hun- dred cities; over the years, it has evolved further through the work of M. Grotschel, S. Hong, M. Junger, P. Miliotis, D. Naddef, M. Padberg, W.R. Pulleyblank, G. Reinelt, G. Rinaldi, and others. We enumerate some of its refinements that led to the solution of a 13,509-city instance. 1991 Mathematics Subject Classification: 90C10 90C27 Keywords and Phrases: traveling salesman; cutting planes The traveling salesman problem, or TSP for short, is easy to state: given a finite number of "cities" along with the cost of travel between each pair of them, find the cheapest way of visiting all of the cities and returning to your starting point. The travel costs are symmetric in the sense that traveling from city X to city Y costs just as much as traveling from Y to X; the "way of visiting all the cities" is simply the order in which the cities are visited. The simplicity of this problem, coupled with its apparent intractability, makes it an ideal platform for exploring new algorithmic ideas. Surveys of work on the TSP can be found in Bellmore and Nemhauser (1968), Lawler, Lenstra, Rinnooy Kan, and Shmoys (1985), Reinelt (1994), and Junger, Reinelt, and Rinaldi (1995). The origins of the TSP are obscure. In the 1920's, the mathematician and economist Karl Menger publicized it among his colleagues in Vienna. In the 1930's, the problem reappeared in the mathematical circles of Princeton. In the 1940's, it was studied by statisticians (Mahalanobis (1940), Jessen (1942)) in connection with an agricultural application and the mathematician Merrill Flood popularized it among his colleagues at the RAND Corporation. Eventually, the TSP gained notoriety as the prototype of a hard problem in combinatorial optimization. A breakthrough came when Dantzig, Fulkerson, and Johnson (1954) published a description of a method for solving the TSP and illustrated the power of this method by solving an instance with 49 cities, an impressive size at that time. Riding the wave of excitement over the numerous applications of the simplex
Recovery of rock climbing performance after surgical reconstruction of finger pulleys

This study evaluated recovery of sport performance and correction of bowstringing after surgical reconstruction of closed finger pulley rupture in high-level rock climbers. A total of 38 patients treated with an extensor retinaculum graft were assessed. The mean follow-up time was 85 months, and 30 patients returned to their previous climbing level. The mean total active motion score was 96% of the opposite side. All patients had an excellent Buck-Gramcko score. There was no significant difference in grip strength and tip pinch strength in the crimp position between the injured side and the opposite side. A total of 31 patients were examined with ultrasonography. In 18, flexor bowstringing effects had returned to near-normal values. There was an association between rock climbing level recovery and the flexor bowstringing correction (odds ratio, 6.9; 95% confidence interval, 1.1–42.8). If flexor bowstringing was corrected, patients were more likely to regain their preinjury sport performance. The ultrasonography measurement was a useful tool for predicting functional recovery. Level of evidence: 4