Miracle-dz/UniFAR-FTUs huggingface dataset:
Overthickening of sedimentary sequences by igneous intrusions

The identification of extensive intrusive igneous complexes in both subsurface data and field studies has led to the quantification of the volumes of igneous material present within sedimentary sequences. Despite this research, however, little connection has been established between the amount of igneous material intruded into a basin and its effect on subsequent basin evolution in terms of burial and loading. We used subsurface data from the Faroe–Shetland Basin to investigate igneous intrusions with the aim of understanding how additional igneous material influences basin evolution. We found that the total estimated thickness of Cretaceous sediments is likely to be an overestimate because the sedimentary fill consists of significant quantities of igneous material emplaced during the Paleocene (56–54 Ma). This additional igneous material has not previously been accounted for in estimates of sedimentation rates and the burial history of the Faroe–Shetland Basin. Petroleum system modelling to understand the generation and expulsion of hydrocarbons benefits from correct estimates of basin fill. The overthickening of basins by igneous material will affect the timing of hydrocarbon generation and therefore the correct evaluation of exploration targets. The volume of igneous material and the time at which this material was emplaced must be acknowledged and considered in order to fully understand basin evolution.
Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB

The conduction mechanism of Escherichia coli AmtB, the structurally and functionally best characterized representative of the ubiquitous Amt/Rh family, has remained controversial in several aspects. The predominant view has been that it facilitates the movement of ammonium in its uncharged form as indicated by the hydrophobic nature of a pore located in the center of each subunit of the homotrimer. Using site-directed mutagenesis and a combination of biochemical and crystallographic methods, we have investigated mechanistic questions concerning the putative periplasmic ammonium ion binding site S1 and the adjacent periplasmic “gate” formed by two highly conserved phenylalanine residues, F107 and F215. Our results challenge models that propose that NH4+ deprotonation takes place at S1 before NH3 conduction through the pore. The presence of S1 confers two critical features on AmtB, both essential for its function: ammonium scavenging efficiency at very low ammonium concentration and selectivity against water and physiologically important cations. We show that AmtB activity absolutely requires F215 but not F107 and that removal or obstruction of the phenylalanine gate produces an open but inactive channel. The phenyl ring of F215 must thus play a very specific role in promoting transfer and deprotonation of substrate from S1 to the central pore. We discuss these results with respect to three distinct mechanisms of conduction that have been considered so far. We conclude that substrate deprotonation is an essential part of the conduction mechanism, but we do not rule out net electrogenic transport.
A randomized controlled trial of high versus low intensity weight training versus general practitioner care for clinical depression in older adults.

BACKGROUND Although exercise has been shown to relieve depression, little is known about its mechanism or dose-response characteristics. We hypothesized that high intensity progressive resistance training (PRT) would be more effective than either low intensity PRT or standard care by a general practitioner (GP) in depressed elderly persons, and that high intensity PRT would provide superior benefits in quality of life, sleep quality, and self-efficacy. METHODS Sixty community-dwelling adults >60 years with major or minor depression were randomized to supervised high intensity PRT (80% maximum load) or low intensity PRT (20% maximum load) 3 days per week for 8 weeks, or GP care. RESULTS A 50% reduction in the Hamilton Rating Scale of Depression score was achieved in 61% of the high intensity, 29% of the low intensity, and 21% of the GP care group (p =.03). Strength gain was directly associated with reduction in depressive symptoms (r = 0.40, p =.004), as was baseline social support network type (F = 3.52, p =.015), whereas personality type, self-efficacy, and locus of control were unrelated to the antidepressant effect. Vitality quality-of-life scale improved more in the high intensity group than in the others (p =.04). Sleep quality improved significantly in all participants (p <.0001), with the greatest relative change in high intensity PRT (p =.05). CONCLUSIONS High intensity PRT is more effective than is low intensity PRT or GP care for the treatment of older depressed patients.
Evaluation of Reuterin Production in Urogenital Probiotic Lactobacillus reuteri RC-14

ABSTRACT Classified as a distinct species in 1980, Lactobacillus reuteri strains have been used in probiotic formulations for intestinal and urogenital applications. In the former, the primary mechanism of action of L. reuteri SD2112 (ATCC 55730) has been purported to be its ability to produce the antibiotic 3-hydroxypropionaldehyde (3-HPA), also known as reuterin. In the vagina, it has been postulated that probiotic Lactobacillus reuteri RC-14 does not require reuterin production but mediates a restoration of the normal microbiota via hydrogen peroxide, biosurfactant, lactic acid production, and immune modulation. The aim of the present study was to determine whether strain RC-14 produced reuterin. Using PCR and DNA dot blot analyses, numerous Lactobacillus species, including RC-14, were screened for the presence of the gene encoding the large subunit of glycerol dehydratase (gldC), the enzyme responsible for reuterin production. In addition, lactobacilli were grown in glycerol-based media and both high-performance liquid chromatography and a colorimetric assay were used to test for the presence of reuterin. L. reuteri RC-14 was determined to be negative for gldC sequences, as well as for the production of reuterin when cultured in the presence of glycerol. These findings support that the probiotic effects of L. reuteri RC-14, repeatedly demonstrated during numerous studies of the intestine and vagina, are independent of reuterin production.
An Experimental Study on Number of Support Vectors in N-bit Parity Problem

Support vector machine (SV machine, SVM) is a genius invention with many merits, such as the non-existence of local minima, the largest separating margins of different clusters, as well as the solid theoretical foundation. However, it is also well-noted that SVMs are frequently with a large number of SVs. In this paper, we investigate the number of SVs in a benchmark problem, the parity problem experimentally. With a large variety of kernel functions, the exhaustive experiments using LibSVM discover that for the N-bit parity problems all 2N points are created as SVs. The study in this paper indicates that the SMO-based LibSVM training candidly incorporate every point in the parity problem. Since any two neighbored points in the N-bit parity problem are with the opposite signs, the SMO creates an SV each time in iterations for fast satisfying the Lagrangian conditions. As a corollary, the SMO-based SVM training is pretty much entangled into the local information and is therefore a greedy algorithm.
Hand2 inhibits kidney specification while promoting vein formation within the posterior mesoderm

Proper organogenesis depends upon defining the precise dimensions of organ progenitor territories. Kidney progenitors originate within the intermediate mesoderm (IM), but the pathways that set the boundaries of the IM are poorly understood. Here, we show that the bHLH transcription factor Hand2 limits the size of the embryonic kidneyby restricting IM dimensions. The IM is expanded in zebrafish hand2 mutants and is diminished when hand2 is overexpressed. Within the posterior mesoderm, hand2 is expressed laterally adjacent to the IM. Venous progenitors arise between these two territories, and hand2 promotes venous development while inhibiting IM formation at this interface. Furthermore, hand2 and the co-expressed zinc-finger transcription factor osr1 have functionally antagonistic influences on kidney development. Together, our data suggest that hand2 functions in opposition to osr1 to balance the formation of kidney and vein progenitors by regulating cell fate decisions at the lateral boundary of the IM. IMPACT STATEMENT The Hand2 transcription factor regulates the dimensions of the kidney by controlling cell fate decisions at the interface between organ fields.
Influence of sonication on the phenolic content and antioxidant activity of Terminalia catappa L. leaves

Aim: This study was designed to evaluate the phenolic content and antioxidant activity of ethanolic extracts from T. catappa leaves obtained by different intervals of sonication. Methods: Three commonly used methods were followed to evaluate phenolic content and four in vitro methods like 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) radical scavenging assay, ferric reducing antioxidant potency (FRAP), and total antioxidant capacity assays for measuring the antioxidant activities. Antioxidant values of these assays were expressed in terms of milligrams vitamin C equivalent (VCE) antioxidant activities. Results: This study showed that extract obtained with 40 minutes of sonication possessed significant (P < 0.05) polyphenolic contents compared to 20 and 60 minutes sonication and control (24 hour maceration). Moreover, sonication of T. catappa leaf above 40 minutes was found to be unsuitable for extracting out phenolic contents. Even the results of antioxidant assays showed that 40 minutes of the sonicated extract exhibited significant (P < 0.05) VCE values compared to extracts obtained at different intervals of sonication and control. Conclusions: In sonication extraction method 40 minutes is an ideal time to obtain extract enriched with high polyphenolic content with good antioxidant activity from T. catappa leaves.
Occupational Lymphohematopoietic Cancer in Korea

The purpose of this study was to review the existing studies on lymphohematopoietic (LHP) cancer in Korea, estimate the prevalence of workers exposed to carcinogens, and determine the population attributable fraction (PAF) of leukemia. Two case series and 4 case reports were reviewed. Using official statistics, the prevalence of benzene exposure and ionizing radiation exposure was estimated. Based on the prevalence of exposure and the relative risk, The PAF of leukemia was calculated. Between 1996 and 2005, 51 cases of LHP cancer were reported from the compensation system. Greater than 50% of occupational LHP cancer was leukemia, and the most important cause was benzene. In a cohort study, the standardized incidence ratio was 2.71 (95% CI, 0.56-7.91). The prevalence of exposure was 2.5% and 2.2% in 1995 and 2000, respectively. Using the 1995 prevalence, 3.6-4.8% and 0.1% of cases with leukemia were attributable to benzene and ionizing radiation exposure, respectively, which resulted in 39.7-51.4 cases per year. Benzene is the most important cause of occupational leukemia in Korea. Considering the estimated PAF in this study, the annual number of occupational LHP cancer (51 cases during 10-yr period), might be underreported within the compensation system.
Aerodynamic Loads on Tall Buildings: Interactive Database

Under the action of wind, tall buildings oscillate simultaneously in the alongwind, acrosswind, and torsional directions. While the alongwind loads have been successfully treated using quasi-steady and strip theories in terms of gust loading factors, the acrosswind and torsional loads cannot be treated in this manner, since these loads cannot be related in a straightforward manner to the fluctuations in the approach flow. Accordingly, most current codes and standards provide little guidance for the acrosswind and torsional response. To fill this gap, a preliminary, interactive database of aerodynamic loads is presented, which can be accessed by any user with Microsoft Explorer at the URL address http://www.nd. edu/;nathaz/. The database is comprised of high-frequency base balance measurements on a host of isolated tall building models. Combined with the analysis procedure provided, the nondimensional aerodynamic loads can be used to compute the wind-induced response of tall buildings. The influence of key parameters, such as the side ratio, aspect ratio, and turbulence characteristics for rectangular sections, is also discussed. The database and analysis procedure are viable candidates for possible inclusion as a design guide in the next generation of codes and standards.
Dual Training and Dual Prediction for Polarity Classification

Bag-of-words (BOW) is now the most popular way to model text in machine learning based sentiment classification. However, the performance of such approach sometimes remains rather limited due to some fundamental deficiencies of the BOW model. In this paper, we focus on the polarity shift problem, and propose a novel approach, called dual training and dual prediction (DTDP), to address it. The basic idea of DTDP is to first generate artificial samples that are polarity-opposite to the original samples by polarity reversion, and then leverage both the original and opposite samples for (dual) training and (dual) prediction. Experimental results on four datasets demonstrate the effectiveness of the proposed approach for polarity classification.
Lai's Conditions for Spanning and Dominating Closed Trails

A graph is supereulerian if it has a spanning closed trail. For an integer $r$, let ${\cal Q}_0(r)$ be the family of 3-edge-connected nonsupereulerian graphs of order at most $r$. For a graph $G$, define $\delta_L(G)=\min\{\max\{d(u), d(v) \}| \ \mbox{ for any $uv\in E(G)$} \}$. For a given integer $p\ge 2$ and a given real number $\epsilon$, a graph $G$ of order $n$ is said to satisfy a Lai's condition if $\delta_L(G)\ge \frac{n}{p}-\epsilon$. In this paper, we show that if $G$ is a 3-edge-connected graph of order $n$ with $\delta_L(G)\ge \frac{n}{p}-\epsilon$, then there is an integer $N(p, \epsilon)$ such that when $n> N(p,\epsilon)$, $G$ is supereulerian if and only if $G$ is not a graph obtained from a graph $G_p$ in the finite family ${\cal Q}_0(3p-5)$ by replacing some vertices in $G_p$ with nontrivial graphs. Results on the best possible Lai's conditions for Hamiltonian line graphs of 3-edge-connected graphs or 3-edge-connected supereulerian graphs are given, which are improvements of the results in [J. Graph Theory 42(2003) 308-319] and in [Discrete Mathematics, 310(2010) 2455-2459].
The Space Between Us: Evaluating a multi-user affective brain-computer music interface

Music as a mechanism for neuro-feedback presents an interesting medium for artistic exploration, especially with regard to passive BCI control. Passive control in a brain-computer music interface (BCMI) provides a means for approximating mental states that can be mapped to select musical phrases, creating a system for real-time musical neuro-feedback. This article presents a BCMI for measuring the affective states of two users, a performer and an audience member, during a live musical performance of the piece titled The Space Between Us. The system adapts to the affective states of the users and selects sequences of a pre-composed musical score. By affect-matching music to mood and subsequently plotting affective musical trajectories across a two-dimensional model of affect, the system attempts to measure the affective interactions of the users, derived from arousal and valence recorded in EEG. An Affective Jukebox, the work of a previous study, validates the method used to read emotions across two dimens.
Fully Covered Self-Expandable Metal Stents for Treatment of Malignant Biliary Strictures due to Pancreatic Carcinoma

Background Transpapillary stents are used to treat malignant biliary strictures. However, there are different stent types and data are controversial in respect to success and complications. Recently, completely covered self-expandable metal stents (CSEMS) have become available. The aim of this study is to present a consecutive series of CSEMS placed to decompress the bile duct in malignant stenosis due to pancreatic carcinoma and to evaluate the effectiveness, complication rate and extractability of these devices. Methods We retrospectively reviewed the courses of 27 consecutive patients who received CSEMS due to malignant biliary strictures because of pancreatic carcinoma regardless of presumed resectability between January 2010 and May 2012 in our endoscopic unit. Results A total of 27 patients (12 male and 15 female) were included in the study. The mean age of the patients was 75 years. Endoscopic retrograde cholangiopancreatography (ERCP), endoscopic sphincterotomy (ES) and stent placement were successful at first attempt in all cases. The mean length of the stenosis was 20 mm. In 24 patients (89%) a stent length of 4 cm was sufficient to bridge the stenosis. In three cases a stent length of 6 cm was necessary. Drainage was achieved as monitored by a significant decrease or normalization of bilirubin in all cases (mean bilirubin 8.5 mg/dL and 1.5 mg/dL before and after stent placement respectively), 15 patients underwent surgery with pylorus preserving duodenopancreatectomy. In all patients who underwent surgery stents could be removed during the operation without difficulties. Leakage of the biliodigestive anastomosis occurred in one patient (6.6%). Four (15%) of the 27 patients developed complications related to the endoscopic procedure and/or stent placement respectively (cholecystitis in two patients, stent occlusion in one patient, and post-sphincterotomy bleeding in one patient). Conclusion The prolonged patency, extractability, and low complication rate of CSEMS make them an attractive treatment option in patients with malignant biliary strictures due to pancreatic carcinoma regardless of resectability.
The computational complexity of linear optics

We give new evidence that quantum computers -- moreover, rudimentary quantum computers built entirely out of linear-optical elements -- cannot be efficiently simulated by classical computers. In particular, we define a model of computation in which identical photons are generated, sent through a linear-optical network, then nonadaptively measured to count the number of photons in each mode. This model is not known or believed to be universal for quantum computation, and indeed, we discuss the prospects for realizing the model using current technology. On the other hand, we prove that the model is able to solve sampling problems and search problems that are classically intractable under plausible assumptions. Our first result says that, if there exists a polynomial-time classical algorithm that samples from the same probability distribution as a linear-optical network, then P#P=BPPNP, and hence the polynomial hierarchy collapses to the third level. Unfortunately, this result assumes an extremely accurate simulation. Our main result suggests that even an approximate or noisy classical simulation would already imply a collapse of the polynomial hierarchy. For this, we need two unproven conjectures: the Permanent-of-Gaussians Conjecture, which says that it is #P-hard to approximate the permanent of a matrix A of independent N(0,1) Gaussian entries, with high probability over A; and the Permanent Anti-Concentration Conjecture, which says that |Per(A)|>=√(n! )poly(n) with high probability over A. We present evidence for these conjectures, both of which seem interesting even apart from our application. This paper does not assume knowledge of quantum optics. Indeed, part of its goal is to develop the beautiful theory of noninteracting bosons underlying our model, and its connection to the permanent function, in a self-contained way accessible to theoretical computer scientists.
Exploring curved anatomic structures with surface sections

The extraction of planar sections from volume images is the most commonly used technique for inspecting and visualizing anatomic structures. We propose to generalize the concept of planar section to the extraction of curved cross-sections (free form surfaces). Compared with planar slices, curved cross-sections may easily follow the trajectory of tubular structures and organs such as the aorta or the colon. They may be extracted from a 3D volume, displayed as a 3D view and possibly flattened. Flattening of curved cross-sections allows to inspect spatially complex relationship between anatomic structures and their neighborhood. They also allow to carry out measurements along a specific orientation. For the purpose of facilitating the interactive specification of free form surfaces, users may navigate in real time within the body and select the slices on which the surface control points will be positioned. Immediate feedback is provided by displaying boundary curves as cylindrical markers within a 3D view composed of anatomic organs, planar slices and possibly free form surface sections. Extraction of curved surface sections is an additional service that is available online as a Java applet (http://visiblehuman.epfl.ch). It may be used as an advanced tool for exploring and teaching anatomy.
Outcome of children born to epileptic mothers treated with carbamazepine during pregnancy.

AIM: The purpose of the study was to assess whether there was an increased rate of congenital anomalies or significant developmental delay in infants of women with epilepsy who had been treated with carbamazepine during pregnancy. METHODS: 47 children were studied, aged 6 months-6 years, who were born to 37 epileptic mothers on carbamazepine monotherapy (group A). All children had a complete physical and neurodevelopmental assessment by a developmental paediatrician, and 41 a complete psychological evaluation. They were compared with 47 children of similar socioeconomic status (group B). RESULTS: Six of the 47 children in group A had typical facial features of 'carbamazepine syndrome'. The average cognitive score of children in group A was significantly lower than in group B. This was mainly because all six children with carbamazepine syndrome had a development quotient or intelligence quotient below 90. There were no differences between the two groups in physical growth or in the rate of major anomalies. Two children in group A had cleft palate but in each case this was found in a parent as well. CONCLUSIONS: In utero exposure to carbamazepine may result in 'carbamazepine syndrome' characterised by facial dysmorphic features and mild mental retardation. Prevalence of carbamazepine syndrome does not seem to be related to the dose of carbamazepine or the presence of maternal convulsions. It may depend upon heredofamilial factors that have yet to be defined. One possible factor is decreased activity of the enzyme epoxide hydrolase with resulting increased concentrations of carbamazepine epoxide which may be teratogenic.
Epidemiological study of eating disorders: time for a change of emphasis

Twenty years have passed since epidemiological methods were first applied to the study of eating disorders. Interest in this approach has been intense in part related to speculation that anorexia nervosa has become more common. In spite of considerable effort research workers have encountered a variety of methodological problems which have left fundamental questions unanswered. Difficulties such as low participation rates, questionable methods of case ascertainment and the study of unrepresentative groups were avoidable. Others are intrinsic to this type of research. Anorexia nervosa is an uncommon disorder and achieving adequate and representative samples outside the hospital setting is difficult. Furthermore, in non-clinical settings eating disorders are often not accompanied by severe weight loss or all features of bulimia nervosa. Clinically derived classification systems are thus rendered of limited use.