Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical significance and effect of Sam68 expression in gastric cancer

Gastric cancer is one of the most common types of malignancy worldwide. However, the molecular mechanisms of cancer development remain unclear. Src-associated in mitosis of 68 kDa (Sam68) is involved in cell proliferation, transformation, tumorigenesis and metastasis in several types of cancer. The present study aimed to assess the expression and function of Sam68 in human gastric cancer. Western blot analysis and immunohistochemistry indicated that Sam68 expression was increased in tumor samples and the levels were associated with the grade of malignancy. High Sam68 expression was associated with the poor prognosis of patients with gastric cancer. In vitro, following knockdown of Sam68 by transfection of gastric cancer cells with small interfering RNA, the cell viability, cell cycle progress, migration and invasion were decreased. The results of the present study revealed that Sam68 may be a novel prognostic factor for, and is associated with cell growth, migration and invasion in, gastric cancer.
Effects of Different Conditioning Activities on 100-m Dash Performance in High School Track and Field Athletes

This study compared the effects of different conditioning activities on the 100-m dash performance of 11 male, high school track and field athletes (mean age = 16.3; SD = 1.2 years). Participants performed a 100-m dash seven minutes after each of four randomized conditioning protocols, with each condition and 100-m dash separated by 3–10 days. The conditioning protocols were (a) control, no conditioning activity; (b) weighted plyometric, three sets of 10 repetitions of alternate leg bounding with additional load of 10% of the body mass; (c) free sprint, two 20-m sprints; and (d) resisted sprint (RS), two 20-m resisted sprints using an elastic tubing tool. We obtained session ratings of perceived exertion (SRPE) immediately after each conditioning protocol. There were no significant differences between any of the three experimental conditioning activities on 100-m sprint time, but the RS protocol improved 100-m sprint time compared with the control (no conditioning) protocol (p < .001). The RS also led to greater sprint velocity and higher SRPE compared with the control condition (p < .01). There was no significant association between SRPE and 100-m performance (p = .77, r = .05). These results suggest a benefit for young male track and field athletes to the elastic tubing warm-up activities prior to the 100-m dash.
Brain morphology and cortical thickness variations in systemic lupus erythematosus patients: Differences among neurological, psychiatric, and nonneuropsychiatric manifestations

To determine whether systemic lupus erythematosus (SLE) affecting subcortical white matter volumes, deep gray matter volumes, and cortical thickness differ between groups of SLE patients with psychiatric (P‐SLE), neurological (N‐SLE), or nonneuropsychiatric (non‐NPSLE) presentations.
Acute effects of caffeine on attention: a comparison of non-consumers and withdrawn consumers

Despite the large number of studies on caffeine and attention, interpretation is often difficult because of methodological weaknesses. In the present study, use of a small battery of tests with four key outcome measures, combined with an appropriate sample size, addresses many of these problems. This methodology was used to examine whether effects of caffeine (a dose of 2 mg/kg) could be explained in terms of reversal of the effects of caffeine withdrawal. This was achieved by examining effects in non-consumers (N = 35), who could not be withdrawn, and also in a group of consumers (N = 35) who had undergone withdrawal for a week and no longer reported symptoms of withdrawal. The results showed no effect of short-term withdrawal on the performance measures, even though subjective reports showed an increase in symptoms after withdrawal. In contrast, the caffeine challenge carried out on Day 8 showed that ingestion of caffeine was associated with faster simple reaction time, fewer long responses, greater detection of targets in the cognitive vigilance task, and faster encoding of new information. These results suggest that it is important to continue to investigate mechanisms underlying these effects of caffeine and to further evaluate the practical implications of such effects.
Effects of a Program for Improving Biomechanical Characteristics During Walking and Running in Children Who Are Obese

Purpose: To investigate the influence of a weight-reduction program with locomotion-emphasis on improving biomechanical characteristics of children who are obese (OW). Methods: Ten children who are OW participated in a 6-month multidisciplinary childhood obesity management program (GRP1); another 10 children who are OW participated in the same multidisciplinary childhood obesity management program with additional locomotion-emphasis exercises for improving biomechanical characteristics (GRP2); and 10 control children who are OW with no intervention program. Outcomes were anthropometric measurements and temporal and foot pressure parameters. Results: GRP2 had significantly improved foot pressure in the different walking/running speeds compared with GRP1. In the temporal parameters, pretests by speed by group interactions were significantly improved for GRP2 compared with GRP1. Conclusions: We found evidence to support beneficial effects of combined dietary and physical activity/locomotion-emphasis exercises on the movement characteristics of children who are OW.
Cytokines, Antibodies, and Histopathological Profiles during Giardia Infection and Variant-Specific Surface Protein-Based Vaccination

ABSTRACT Giardiasis is one of the most common human intestinal diseases worldwide. Several experimental animal models have been used to evaluate Giardia infections, with gerbils (Meriones unguiculatus) being the most valuable model due to their high susceptibility to Giardia infection, abundant shedding of cysts, and pathophysiological alterations and signs of disease similar to those observed in humans. Here, we report cytokine and antibody profiles both during the course of Giardia infection in gerbils and after immunization with a novel oral vaccine comprising a mixture of purified variant-specific surface proteins (VSPs). Transcript levels of representative cytokines of different immune profiles as well as macro- and microtissue alterations were assessed in Peyer's patches, mesenteric lymph nodes, and spleens. During infection, cytokine responses showed a biphasic profile: an early induction of Th1 (gamma interferon [IFN-γ], interleukin-1β [IL-1β], IL-6, and tumor necrosis factor [TNF]), Th17 (IL-17), and Th2 (IL-4) cytokines, together with intestinal alterations typical of inflammation, followed by a shift toward a predominant Th2 (IL-5) response, likely associated with a counterregulatory mechanism. Conversely, immunization with an oral vaccine comprising the entire repertoire of VSPs specifically showed high levels of IL-17, IL-6, IL-4, and IL-5, without obvious signs of inflammation. Both immunized and infected animals developed local (intestinal secretory IgA [S-IgA]) and systemic (serum IgG) humoral immune responses against VSPs; however, only infected animals showed evident signs of giardiasis. This is the first comprehensive report of cytokine expression and anti-Giardia antibody production during infection and VSP vaccination in gerbils, a reliable model of the human disease.
Locally Indecomposable Galois Representations

Abstract In a previous paper the authors showed that, under some technical conditions, the local Galois representations attached to the members of a non- $\text{CM}$ family of ordinary cusp forms are indecomposable for all except possibly finitely many members of the family. In this paper we use deformation theoretic methods to give examples of non- $\text{CM}$ families for which every classical member of weight at least two has a locally indecomposable Galois representation.
Metabolically distinct weight loss by 10,12 CLA and caloric restriction highlight the importance of subcutaneous white adipose tissue for glucose homeostasis in mice

Background Widely used as a weight loss supplement, trans-10,cis-12 conjugated linoleic acid (10,12 CLA) promotes fat loss in obese mice and humans, but has also been associated with insulin resistance. Objective We therefore sought to directly compare weight loss by 10,12 CLA versus caloric restriction (CR, 15–25%), an acceptable healthy method of weight loss, to determine how 10,12 CLA-mediated weight loss fails to improve glucose metabolism. Methods Obese mice with characteristics of human metabolic syndrome were either supplemented with 10,12 CLA or subjected to CR to promote weight loss. Metabolic endpoints such as energy expenditure, glucose and insulin tolerance testing, and trunk fat distribution were measured. Results By design, 10,12 CLA and CR caused equivalent weight loss, with greater fat loss by 10,12 CLA accompanied by increased energy expenditure, reduced respiratory quotient, increased fat oxidation, accumulation of alternatively activated macrophages, and browning of subcutaneous white adipose tissue (WAT). Moreover, 10,12 CLA-supplemented mice better defended their body temperature against a cold challenge. However, 10,12 CLA concurrently induced the detrimental loss of subcutaneous WAT without reducing visceral WAT, promoted reduced plasma and WAT adipokine levels, worsened hepatic steatosis, and failed to improve glucose metabolism. Obese mice undergoing CR were protected from subcutaneous-specific fat loss, had improved hepatic steatosis, and subsequently showed the expected improvements in WAT adipokines, glucose metabolism and WAT inflammation. Conclusions These results suggest that 10,12 CLA mediates the preferential loss of subcutaneous fat that likely contributes to hepatic steatosis and maintained insulin resistance, despite significant weight loss and WAT browning in mice. Collectively, we have shown that weight loss due to 10,12 CLA supplementation or CR results in dramatically different metabolic phenotypes, with the latter promoting a healthier form of weight loss.
A comparison of presettlement and modern forest composition along an elevation gradient in central New Hampshire

Tree species composition is influenced not only by edaphic and climatic factors, but also by natural and humancaused disturbances. To understand interactions among these influences, we compared forest species composition data from the time of European settlement with modern data. We derived elevation data for 2,529 trees mapped by early land surveys (1770-1850) across a 1,000-m elevation gradient in central New Hampshire, and compared these with modern data (2004-9) from the Forest Inventory and Analysis program (123 plots containing 2126 trees), and from permanent plots representing case studies of different land-use histories. Spruce and beech are much less abundant today at all elevations than they were prior to settlement, while maples and birches have increased. Fir, hemlock, pines, and oaks have changed little in distribution, though pines and oaks increased in abundance somewhat. Land-use history (agriculture below 500 m and cutting of various intensities at all elevations) is likely the primary explanation for these shifts, though climate change is also an important factor for some. A clearer understanding of presettlement forest composition improves our ability to separate the relative importance of natural and human-driven influences on the species composition of today’s forests. __________________________ This reformatted accepted manuscript is made available by the authors, in accordance with the author rights policy of NRC Research Press. The formatted final version is available from the publisher at http://dx.doi. org/10.1139/10.1139/x11-169 This document should be cited as: Vadeboncoeur, M.A., S.P. Hamburg, C. V Cogbill, and W.Y. Sugimura. 2012. A comparison of presettlement and modern forest composition along an elevation gradient in central New Hampshire. Canadian Journal of Forest Research 42(1): 190–202. Vadeboncoeur et al. 2012 Presettlement and modern forest composition in central NH [postprint]
Context dependent neuroprotective properties of prion protein (PrP)

Although it has been known for more than twenty years that an aberrant conformation of the prion protein (PrP) is the causative agent in prion diseases, the role of PrP in normal biology is undetermined. Numerous studies have suggested a protective function for PrP, including protection from ischemic and excitotoxic lesions and several apoptotic insults. On the other hand, many observations have suggested the contrary, linking changes in PrP localization or domain structure—independent of infectious prion conformation—to severe neuronal damage. Surprisingly, a recent report suggests that PrP is a receptor for toxic oligomeric species of a-β, a pathogenic fragment of the amyloid precursor protein, and likely contributes to disease pathogenesis of Alzheimer’s disease. We sought to access the role of PrP in diverse neurological disorders. First, we confirmed that PrP confers protection against ischemic damage using an acute stroke model, a well characterized association. After ischemic insult, PrP knockouts had dramatically increased infarct volumes and decreased behavioral performance compared to controls. To examine the potential of PrP’s neuroprotective or neurotoxic properties in the context of other pathologies, we deleted PrP from several transgenic models of neurodegenerative disease. Deletion of PrP did not substantially alter the disease phenotypes of mouse models of Parkinson’s disease or tauopathy. Deletion of PrP in one of two Huntington’s disease models tested, R6/2, modestly slowed motor deterioration as measured on an accelerating rotarod but otherwise did not alter other major features of the disease. Finally, transgenic overexpression of PrP did not exacerbate the Huntington’s motor phenotype. These results suggest that PrP has a context-dependent neuroprotective function and does not broadly contribute to the disease models tested herein.
The Fiber Bundle Model: Modeling Failure in Materials

Description: The book contains different applications of the fiber bundle model. As example, the authors have included fatigue and creep in their discussion. The understanding of materials and their behavior under different conditions is undergoing a revolution due to the coming–of–age of computational atomistic modeling. Even though this technique allows for the precise knowledge of what every atom is doing in such materials, it is still necessary to understand the results in terms of models such as the fiber bundle model. From the contents: The Fiber Bundle Model Average Properties Fluctuation Effects Local and Intermediate Load Sharing Recursive Breaking Dynamics Predicting Failure Fiber Bundle Model in Material Science Snow Avalanches and Landslides
Late Cretaceous‐Tertiary tectonics of the southwest Pacific: Insights from U‐Pb sensitive, high‐resolution ion microprobe (SHRIMP) dating of eclogite facies rocks from New Caledonia

We present new U‐Pb sensitive, high‐resolution ion microprobe (SHRIMP) dates for zircon from eclogite facies samples from northern New Caledonia, which have important consequences for the Late Cretaceous to Eocene tectonic evolution of the southwest Pacific region. Two high‐pressure metapelites contain zoned zircon crystals. Cores of these crystals represent inherited magmatic zircon grains, which yield an age of 85 Ma in both samples. Igneous zircon domains from a metamorphosed mafic cumulate and a felsic metasedimentary rock were also dated at 55 Ma. The igneous zircon of uniform age in rocks of sedimentary origin indicates that sedimentation took place from a restricted source area soon after magmatism. Therefore the protoliths of the eclogite facies rocks are considered to have formed between 85 and 55 Ma in a back‐arc basin. This time period matches the age of the unmetamorphosed Poya Terrane of western New Caledonia and provides further evidence for a direct link between the two terranes. In the metapelites, irregular zircon rims that cross cut the oscillatory zoning of the cores have low trace element and Th/U contents and contain inclusions of high‐pressure minerals providing evidence that these zircon rims formed during eclogite facies metamorphism. Therefore the 44.1 ± 0.9 Ma and 44.5 ± 1.2 Ma ages obtained from these rims represent burial related to subduction of the back‐arc basin. It is suggested that subduction initiated soon after deposition of the youngest sediments at 55 Ma and stopped at 44 Ma during attempted subduction of continental crust, now represented as the Norfolk Ridge. Therefore the subduction system that produced the high‐pressure rocks could only have operated for a maximum of 11 m.y. and would have been relatively hot. The 44 Ma age constraint for peak metamorphism also significantly predates (by 10 m.y.) the timing of obduction of the New Caledonia Ultramafic Nappe, discounting any link between obduction and high‐pressure metamorphism. Combining our results with previously documented geological data, we present a revised model for the geological development of New Caledonia, which involves multiple episodes of compression and extension during the Eocene.
The Importance of Coral Larval Recruitment for the Recovery of Reefs Impacted by Cyclone Yasi in the Central Great Barrier Reef

Cyclone Yasi, one of the most severe tropical storms on record, crossed the central Great Barrier Reef (GBR) in February 2011, bringing wind speeds of up to 285 km hr−1 and wave heights of at least 10 m, and causing massive destruction to exposed reefs in the Palm Island Group. Following the cyclone, mean (± S.E.) hard coral cover ranged from just 2.1 (0.2) % to 5.3 (0.4) % on exposed reefs and no reproductively mature colonies of any species of Acropora remained. Although no fragments of Acropora were found at impacted exposed sites following the cyclone, small juvenile colonies of Acropora (<10 cm diameter) were present, suggesting that their small size and compact morphologies enabled them to survive the cyclone. By contrast, sheltered reefs appeared to be unaffected by the cyclone. Mean (± S.E.) hard coral cover ranged from 18.2 (2.4) % to 30.0 (1.0) % and a large proportion of colonies of Acropora were reproductively mature. Macroalgae accounted for 8 to 16% of benthic cover at exposed sites impacted by cyclone Yasi but were absent at sheltered sites. Mean (± S.E.) recruitment of acroporids to settlement tiles declined from 25.3 (4.8) recruits tile−1 in the pre-cyclone spawning event (2010) to 15.4 (2.2) recruits tile−1 in the first post-cyclone spawning event (2011). Yet, post-cyclone recruitment did not differ between exposed (15.2±2.1 S.E.) and sheltered sites (15.6±2.2 S.E.), despite the loss of reproductive colonies at the exposed sites, indicating larval input from external sources. Spatial variation in impacts, the survival of small colonies, and larval replenishment to impacted reefs suggest that populations of Acropora have the potential to recover from this severe disturbance, provided that the Palm Islands are not impacted by acute disturbances or suffer additional chronic stressors in the near future.
Impulsive Control for G-AIMD Dynamics with Relaxed and Hard Constraints

Motivated by various applications from Internet congestion control to power control in smart grids and electric vehicle charging, we study Generalized Additive Increase Multiplicative Decrease (G-AIMD) dynamics under impulsive control in continuous time with the time average alpha-fairness criterion. We first show that the control under relaxed constraints can be described by a threshold. Then, we propose a Whittle-type index heuristic for the hard constraint problem. We prove that in the homogeneous case the index policy is asymptotically optimal when the number of users is large.
Relation between Skin Pharmacokinetics and Efficacy in AmBisome Treatment of Murine Cutaneous Leishmaniasis

ABSTRACT AmBisome (LAmB), a liposomal formulation of amphotericin B (AmB), is a second-line treatment for the parasitic skin disease cutaneous leishmaniasis (CL). Little is known about its tissue distribution and pharmacodynamics to inform clinical use in CL. Here, we compared the skin pharmacokinetics of LAmB with those of the deoxycholate form of AmB (DAmB; trade name Fungizone) in murine models of Leishmania major CL. Drug levels at the target site (the localized lesion) 48 h after single intravenous (i.v.) dosing of the individual AmB formulations (1 mg/kg of body weight) were similar but were 3-fold higher for LAmB than for DAmB on day 10 after multiple administrations (1 mg/kg on days 0, 2, 4, 6, and 8). After single and multiple dosing, intralesional concentrations were 5- and 20-fold, respectively, higher than those in the healthy control skin of the same infected mice. We then evaluated how drug levels in the lesion after LAmB treatment relate to therapeutic outcomes. After five administrations of the drug at 0, 6.25, or 12.5 mg/kg (i.v.), there was a clear correlation between dose level, intralesional AmB concentration, and relative reduction in parasite load and lesion size (R2 values of >0.9). This study confirms the improved efficacy of the liposomal over the deoxycholate AmB formulation in experimental CL, which is related to higher intralesional drug accumulation.
Pinning Control of Uncertain Complex Networks to a Homogeneous Orbit

A sufficient condition for the stability of uncertain complex networks is derived in terms of linear matrix inequalities based on the V-stability tool, which associates the self-dynamics of nodes with passivity degrees. Then, a pinning control strategy is proposed on the developed condition to stabilize the uncertain complex networks to a homogenous orbit. As an illustrative example, a network with the Lorenz system as node self-dynamics is simulated to verify the analytic results.
Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016

Abstract Information retrieval from biomedical repositories has become a challenging task because of their increasing size and complexity. To facilitate the research aimed at improving the search for relevant documents, various information retrieval challenges have been launched. In this article, we present the improved medical information retrieval systems designed by Poznan University of Technology and Poznan University of Medical Sciences as a contribution to the bioCADDIE 2016 challenge—a task focusing on information retrieval from a collection of 794 992 datasets generated from 20 biomedical repositories. The system developed by our team utilizes the Terrier 4.2 search platform enhanced by a query expansion method using word embeddings. This approach, after post-challenge modifications and improvements (with particular regard to assigning proper weights for original and expanded terms), allowed us achieving the second best infNDCG measure (0.4539) compared with the challenge results and infAP 0.3978. This demonstrates that proper utilization of word embeddings can be a valuable addition to the information retrieval process. Some analysis is provided on related work involving other bioCADDIE contributions. We discuss the possibility of improving our results by using better word embedding schemes to find candidates for query expansion. Database URL: https://biocaddie.org/benchmark-data