Miracle-dz/UniFAR-FTUs huggingface dataset:
Titration in silico of reversible B <=> A transitions in DNA.

Reversible transitions between the A- and B-forms of DNA are obtained in free molecular dynamics simulations of a single double helix immersed in a water drop with Na(+) counterions. The dynamics of the transitions agrees with their supposed cooperative character. In silico titration of the transitions was carried out by smooth variation of the drop size. The estimated range of hydration numbers corresponding to the transition roughly agrees with experimental data. The chain length dependence was studied for double helices from 6 to 16 base pairs. It appeared that the B --> A transition is hindered for DNA shorter than one helical turn. With increased NaCl concentration in the drop, stabilization of the B-form is observed accompanied by the salt crystallization. The results strongly suggest that the B --> A transition at low hydration is caused by Na(+) ions sandwiched between phosphate strands in the major groove and is driven by direct medium range electrostatic interactions. The role of the reduced water shell apparently consists of increasing the counterion concentration in the opening of the major groove. Analysis of the available experimental data suggests that this mechanism is perhaps generally responsible for the A/B polymorphism in DNA.
Involvement of platelet‐activating factor and LIS1 in neuronal migration

Platelet‐activating factor (PAF, 1‐O‐alkyl‐2‐acetyl‐sn‐glycero‐3‐phosphocholine) is a biologically active lipid mediator. We have previously shown the expression of PAF receptor in neurons and microglia. PAF is produced in the brain from its precursor, and degraded by the enzyme PAF acetylhydrolase. LIS1 is a regulatory subunit of PAF acetylhydrolase, and is identical to a gene whose deletion causes the human neuronal migration disorder, type I lissencephaly. Indeed, Lis1 mutant mice display defects in neuronal migration and layering in vivo, and also in cerebellar granule cell migration in vitro. However, the roles of PAF and the PAF receptor in the neuronal migration remain to be determined. Here, we show that PAF receptor‐deficient mice exhibited histological abnormalities in the embryonic cerebellum. PAF receptor‐deficient cerebellar granule neurons migrated more slowly in vitro than wild‐type neurons, consistent with the observation that a PAF receptor antagonist reduced the migration of wild‐type neurons in vitro. Synergistic reduction of neuronal migration was observed in a double mutant of PAF receptor and LIS1. Unexpectedly, PAF affected the migration of PAF receptor‐deficient neurons, suggesting a receptor‐independent pathway for PAF action. The PAF receptor‐independent response to PAF was abolished in granule neurons derived from the double mutant mice. Thus, our results suggest that the migration of cerebellar granule cells is regulated by PAF through receptor‐dependent and receptor‐independent pathways, and that LIS1 is a pivotal molecule that links PAF action and neuronal cell migration both in vivo and in vitro.
Insulin Release in RINm5F Cells and Glyceraldehyde Activation of Protein Kinase C

In the insulin-secreting, glucose-insensitive islet cell subclone RINm5F, the distribution of protein kinase C (PKC) activity in the cytosol and membrane fractions was determined, and the activation of the enzyme, as reflected in its translocation to the membrane fraction, was characterized in conjunction with insulin release. DL-Glyceraldehyde (15 mM) evoked a rapid redistribution of PKC from the cytosol to the membrane fraction; insulin release increased concomitantly. When monitored over 5 min with 15 mM glyceraldehyde, membrane stabilization of PKC reached a maximum at 30 s and decreased thereafter; insulin release occurred at a high rate for the first 15 s and diminished thereafter. With 2–20 mM glyceraldehyde, a dose-dependent increase in membrane stabilization of PKC occurred and was accompanied by a matching increase in insulin release. Exogenous 1,2-dioctanoyl-sn-glycerol (100 μM) induced a rapid membrane stabilization of PKC and concomitant stimulation of insulin release. Glucose (15 mM) failed to evoke any redistribution of PKC or release of insulin. Depletion of total PKC activity by 95% induced by 18-h incubations with 2 μM 12-O-tetradecanoylphorbol-13-acetate resulted in a 67–91% reduction in glyceraldehyde-induced insulin release. We conclude that in the RINm5F islet β-cell subclone 7) the rapid activation of PKC, which occurs in response to the administration of glyceraldehyde, a nutrient secretagogue, plays an amplifying role in the initiation of stimulated insulin release; and 2) the failure of the activation of PKC may be responsible for the insensitivity to glucose.
Skin aging: are adipocytes the next target?

Dermal white adipose tissue (dWAT) is increasingly appreciated as a special fat depot. The adipocytes in this depot exert a variety of unique effects on their surrounding cells and can undergo massive phenotypic changes. Significant modulation of dWAT content can be observed both in intrinsically and extrinsically aged skin. Specifically, skin that has been chronically photo-damaged displays a reduction of the dWAT volume, caused by the replacement of adipocytes by fibrotic structures. This is likely to be caused by the recently uncovered process described as “adipocyte-myofibroblast transition” (AMT). In addition, contributions of dermal adipocytes to the skin aging processes are also indirectly supported by spatial correlations between the prevalence of hypertrophic scarring and the appearance of signs of skin aging in different ethnic groups. These observations could elevate dermal adipocytes to prime targets in strategies aimed at counteracting skin aging.
Temporal Dynamics of Stress-Induced Alternations of Intrinsic Amygdala Connectivity and Neuroendocrine Levels

Stress-induced changes in functional brain connectivity have been linked to the etiology of stress-related disorders. Resting state functional connectivity (rsFC) is especially informative in characterizing the temporal trajectory of glucocorticoids during stress adaptation. Using the imaging Maastricht Acute Stress Test (iMAST), we induced acute stress in 39 healthy volunteers and monitored the neuroendocrine stress levels during three runs of resting state functional magnetic resonance imaging (rs-fMRI): before (run 1), immediately following (run 2), and 30min after acute stress (run 3). The iMAST resulted in strong increases in cortisol levels. Whole-brain analysis revealed that acute stress (run 2 - 1) was characterized by changes in connectivity of the amygdala with the ventrolateral prefrontal cortex (vlPFC), ventral posterior cingulate cortex (PCC), cuneus, parahippocampal gyrus, and culmen. Additionally, cortisol responders were characterized by enhanced amygdala - medial prefrontal cortex (mPFC) connectivity. Stress recovery (run 3 - 2) was characterized by altered amygdala connectivity with the dorsolateral prefrontal cortex (dlPFC), ventral and dorsal anterior cingulate cortex (ACC), anterior hippocampal complex, cuneus, and presupplementary motor area (preSMA). Opposite to non-responders, cortisol responders were characterized by enhanced amygdala connectivity with the anterior hippocampal complex and parahippocampal gyrus, and reduced connectivity with left dlPFC, dACC, and culmen during early recovery. Acute stress responding and recovery are thus associated with changes in the functional connectivity of the amygdala network. Our findings show that these changes may be regulated via stress-induced neuroendocrine levels. Defining stress-induced neuronal network changes is pertinent to developing treatments that target abnormal neuronal activity.
Origin of the ahead of tsunami traveling ionospheric disturbances during Sumatra tsunami and offshore forecasting

The presence of ionospheric disturbances associated with Sumatra 2004 tsunami that propagated ahead of tsunami itself has previously been identified. However, their origin remains unresolved till date. Focusing on their origin mechanism, we document these ionospheric disturbances referred as Ahead of tsunami Traveling Ionospheric Disturbances (ATIDs). Using total electron content (TEC) data from GPS Aided GEO Augmented Navigation GPS receivers located near the Indian east coast, we first confirm the ATIDs presence in TEC that appear ~90 min ahead of the arrival of tsunami at the Indian east coast. We propose here a simulation study based on tsunami‐atmospheric‐ionospheric coupling that considers tsunamigenic acoustic gravity waves (AGWs) to excite these disturbances. We explain the ATIDs generation based on the dissipation of transverse mode of the primary AGWs. The simulation corroborates the excitation of ATIDs with characteristics similar to the observations. Therefore, we offer an alternative theoretical tool to monitor the offshore ATIDs where observations are either rare or not available and could be potentially important for the tsunami early warning.
Multilingual Language Processing From Bytes

We describe an LSTM-based model which we call Byte-to-Span (BTS) that reads text as bytes and outputs span annotations of the form [start, length, label] where start positions, lengths, and labels are separate entries in our vocabulary. Because we operate directly on unicode bytes rather than language-specific words or characters, we can analyze text in many languages with a single model. Due to the small vocabulary size, these multilingual models are very compact, but produce results similar to or better than the state-of- the-art in Part-of-Speech tagging and Named Entity Recognition that use only the provided training datasets (no external data sources). Our models are learning "from scratch" in that they do not rely on any elements of the standard pipeline in Natural Language Processing (including tokenization), and thus can run in standalone fashion on raw text.
Late Neogene Sirius Group strata in Reedy Valley, Antarctica: a multiple-resolution record of climate, ice-sheet and sea-level events

Abstract Late Neogene Sirius Group strata from Tillite Spur and Quartz Hills in the Reedy Glacier area, Antarctica, demonstrate the variability in Sirius Group facies and contrasts Sirius Group strata deposited at high and low paleo-elevation, respectively. The Tillite Spur and Quartz Hills Formations (Pliocene) are formally defined here.The Tillite Spur Formation type section crops out on the edge of the Wisconsin Plateau overlooking Tillite Spur. It comprises 32m of alternating coarse gray conglomerate and muddy olive-brown diamictites. The Quartz Hills Formation type section crops out above the western margin of Reedy Glacier in a pre-existing cirque towards the southern end of the Quartz Hills. It comprises c.100m of alternating massive diamictites and rhythmically interbedded sandstone and laminated mudstones which were deposited close to sea level and subsequently rapidly uplifted (>500 m Myr−1) to their present elevation at c. 1500 m. Three orders of paleoclimatic variability are recorded in the Sirius Group strata from Reedy Valley: (1) recycled marine microfloras in glacial diamictites indicate intervals of marine incursion into the Antarctic cratonic interior co-occurring with reductions in the East Antarctic ice sheet; (2) an advancing and retreating paleo-Reedy Glacier deposited a glacial/interglacial sequence alternating on a 10-100 kyr scale; 3) Centimeter and millimeter stratification in strata of the Quartz Hills Formation record annual kyr scale variability.
Effects of cigarette smoking on tissue gas exchange during hyperbaric exposures.

OBJECTIVES In this study we investigate whether differences exist in human skeletal muscle (MM) and subcutaneous (SC) tissue gas tensions between chronic cigarette smokers and non-smokers measured under room air and hyperbaric conditions. METHODS Gas tensions in resting MM and SC tissues were recorded using a mass spectrometer at four-minute intervals during two and one-half to three-hour period in smokers and non-smokers during normobaric, normoxic (room air) and hyperbaric conditions. Two hyperbaric oxygen (HBO2) protocols were utilized: Protocol A employed the continuous breathing of oxygen (O2) at 2 ATA, a typical monoplace hyperbaric chamber treatment, while Protocol B utilized intermittent air breaks between O2 breathing periods at 2 ATA representative of a multiplace hyperbaric chamber treatment. RESULTS All tissue gas tensions changed significantly (repeated measures of variance, p=0.00001) with time as pressures and gas mixtures breathed were altered. Significant Individual Step Analysis (ISA) differences occurred with unloading of nitrogen (N2) from the muscle compartment in both protocols (T-test and Wilcoxon Rank Sum). The interaction of grouping variable and time revealed significant differences between smokers and non-smokers in unloading MM N2 in both protocols: Protocol A (p=0.02) and in Protocol B (p=0.022). Carbon dioxide (CO2) levels in both protocols decreased significantly with time when exposed to HBO2 while increasing when breathing air at 2 ATA. CONCLUSIONS This study demonstrates: 1) Smokers release MM N2 more slowly than nonsmokers during hyperbaric oxygen exposures regardless of the treatment protocol used; 2) There were no significant differences in O2 loading of MM and SC tissues during HBO2 exposures between smokers and nonsmokers; 3) The CO2 levels in both protocols decrease with time when exposed to HBO2 while increasing with breathing air at 2 ATA; 4) The known vasoconstriction effect in subcutaneous tissue from nicotine lasts less than one hour with the topical adiabatic heating increasing the O2 loading specifically in the SC tissues of smokers; 5) Wounds heal more slowly due to the chronically injured endothelium from carbon monoxide, hydrogen cyanide, and other toxic products in smoke rather than from the transient elevations of nicotine.
Sliding-window caching algorithm for streaming media server

In the paper, we propose a novel Sliding Window caching algorithm for fast interactive access to alleviating the bottleneck in accessing disk I/O or network of limited bandwidth, which uses periodic caching to efficiently manage the cached video data. The performance is further enhanced by adopting two policies: prefix caching and variable-sized caching. Simulations using traces from a real VOD server confirm that our proposed method considerably outperforms existing techniques based on uniform segmentation, exponential segmentation, LRU exponential segmentation and adaptive and lazy segmentation algorithm. Under VCR operations, our proposed method achieves a 35% disk load reduction by caching 2.4% of the video' total size.
Assessment of Metal Contamination in Coastal Sediments of the Lévrier Bay Area, Atlantic Ocean, Mauritania

This work presents an assessment of marine pollution due to heavy metals accumulated in surface sediments collected from the Lévrier bay coastline in NW Atlantic, Mauritania. The samples were subjected to HCl and HNO3 digestion, and an atomic absorption spectrophotometer was used to determine the concentrations of all metals (Cd, Pb, Cu and Zn) with the exception of Hg that was analysed by DMA-80 Direct Mercury Analyzer. The ranking of the metals at all studied sites was Al>Zn > Cu >Pb> Cd>Hg, and all the sediments samples displayed lower concentrations than the calculated worldwide mean of unpolluted sediments. The data were classified according to seasons. Eight common pollution indices (i.e. EF, Igeo, QoC(%), CF, SPI, PLI, Cd and PERI)were applied to ascertain the sediment quality. The enrichment (EF) factor resulting from Pb, Cu and Zn were <1 in surface sediments at all sampling sites and for Cd at Cap Blanc, indicating no enrichement . EF values in COMECA and Baie de l'Etoile for Cd were 1 < EF < 3, indicating a low enrichment. EF values for Cd at IMROP were 3 < EF < 5 indicated a moderate enrichment. The value of the geoaccumulation (Igeo) factor from all metals analysed was less than 0 in all sampling sites, which classified the sediments as uncontaminated.The value of contamination (CF) factor for all elements analyzed was lower than 1 across all sampling sites, implying a low contamination.The values of Sediment Pollution (SPI) Index were 0<SPI<2, indicating a natural status of sediments in COMECA, Baie de l'Etoile and Cap Blanc. The SPI values at IMROP were 2<SPI<5, which showed a low pollution of sediments on this site. The value of the pollution load (PLI) index was <1, which indicated that no metal pollution existed in sediments in all studied sites. The values of the contamination degree (Cd) were <6 in all sampling sites, indicating a low degree of contamination. The values of the Potential Ecological Risk (PERI) index were 21.5<PERI <28.4 in all sampling sites, indicating a low ecologic risk.These results provide an important reference for future comparisons in the West African sub-region on the state of contamination of marine and coastal areas. Key-words: Heavy metals, Pollution indexes, Sediments, Lévrier bay, Mauritania. Department of Biology, Faculty of Science and Technology, UR / EBIOME, University of Nouakchott AL Aasriya, Mauritania legraahoussein@yahoo.fr , mintsidoumou@yahoo.fr , hmd108@yahoo.fr Department of Geology, Faculty of Science and Technology, University of Nouakchott AL Aasriya, Mauritania saleckakm@yahoo.fr National Office for Sanitary Inspection of Fisheries and Aquaculture Products (ONISPA), Mauritania alydartige@yahoo.fr, cheikhzamel@gmail.com Department of Earth Sciences, Faculty of Science and Technology, Laboratory of Environmental Geosciences, Abdelmalek Essaidi University, Tétouan, Morocco h.erraioui@fstt.ac. ma
CTRP3/cartducin is induced by transforming growth factor‐β1 and promotes vascular smooth muscle cell proliferation

CTRP3 (C1q and tumour necrosis factor‐related protein 3)/cartducin, a novel serum protein, is a member of the CTRP superfamily. Although the CTRP3/cartducin gene is markedly up‐regulated in rat carotid arteries after balloon injury, little is known about its biological roles in arterial remodelling and neointima formation in injured blood vessels. We have investigated the mechanisms underlying CTRP3/cartducin up‐regulation and the in vitro effects of CTRP3/cartducin on vascular smooth muscle cells. CTRP3/cartducin expression in cultured p53LMAC01 vascular smooth muscle cells was induced by TGF‐β1 (transforming growth factor‐β1), but not by bFGF (basic fibroblast growth factor) or PDGF‐BB (platelet‐derived growth factor‐BB). Exogenous CTRP3/cartducin promoted the proliferation of p53LMAC01 cells in a dose‐dependent manner via ERK1/2 (extracellular signal‐regulated kinase 1/2)‐ and MAPK (p38 mitogen‐activated protein kinase)‐signalling pathways. In contrast, CTRP3/cartducin exhibited no effect on the migration of p53LMAC01 cells. Taken together, the results of the present study demonstrate a novel biological role of CTRP3/cartducin in promoting vascular smooth muscle cell proliferation in blood vessel walls after injury.
A Short-Term Evaluation of Project Dare (Drug Abuse Resistance Education): Preliminary Indications of Effectiveness

This short-term evaluation was designed to assess the impact of Project DARE (Drug Abuse Resistance Education), a joint project of the Los Angeles Police Department and the Los Angeles Unified School District, on the knowledge, attitudes, and self-reported behavior of seventh-grade children who received the full-semester DARE curriculum during sixth grade. Compared to a control group, students who had DARE training reported significantly lower use of alcohol, cigarettes, and other drugs since graduating from sixth grade. These findings were especially strong for boys. In response to questions for which students were to imagine friends pressuring them to use alcohol or drugs, DARE students refused the imagined offers more frequently and more often used refusal strategies that removed them from the immediate temptation.
In Vitro versus In Vivo Phase Instability of Zirconia-Toughened Alumina Femoral Heads: A Critical Comparative Assessment

A clear discrepancy between predicted in vitro and actual in vivo surface phase stability of BIOLOX®delta zirconia-toughened alumina (ZTA) femoral heads has been demonstrated by several independent research groups. Data from retrievals challenge the validity of the standard method currently utilized in evaluating surface stability and raise a series of important questions: (1) Why do in vitro hydrothermal aging treatments conspicuously fail to model actual results from the in vivo environment? (2) What is the preponderant microscopic phenomenon triggering the accelerated transformation in vivo? (3) Ultimately, what revisions of the current in vitro standard are needed in order to obtain consistent predictions of ZTA transformation kinetics in vivo? Reported in this paper is a new in toto method for visualizing the surface stability of femoral heads. It is based on CAD-assisted Raman spectroscopy to quantitatively assess the phase transformation observed in ZTA retrievals. Using a series of independent analytical probes, an evaluation of the microscopic mechanisms responsible for the polymorphic transformation is also provided. An outline is given of the possible ways in which the current hydrothermal simulation standard for artificial joints can be improved in an attempt to reduce the gap between in vitro simulation and reality.
Empirical validation of closed population abundance estimates and spatially explicit density estimates using a censused population of North American red squirrels

Capture-mark-recapture (CMR) data is widely used to estimate a range of population parameters including abundance and density. Closed population estimators have gained wide acceptance and have become increasingly sophisticated. More recently, spatially explicit capture-recapture (SECR) models implemented have gained popularity. Although model accuracy has been tested via simulation studies there have been few empirical tests of either method. I took advantage of a fully enumerated population of red squirrels (Tamiasciurus hudsonicus) to test the accuracy of closed population abundance estimator and the maximum likelihood SECR density estimator. I found abundance estimates were positively biased by 45%, largely due to trapping grid edge effects. Adjusting for edge effects via the boundary strip method decreased bias to -22%. With the addition of inter-trap movements, SECR models produced density estimates that were negatively biased by only 4.6%. These empirical validations support the use of SECR models for density estimates or derived population abundance.
Isolated versus Pierre Robin Sequence Cleft Palates: Are They Different?

Objective To determine if there are any differences in size between isolated cleft palates (CPs) and those associated with Pierre Robin (PR) sequence. Study Design Prospective case series. Settings Tertiary care hospital. Subjects and Methods From 1993 to 2011, nonsyndromic isolated CP and PR sequence cases were classified as severe if the patients had respiratory or feeding difficulties. While patients were under general anesthesia, seven anatomical cleft parameters were prospectively measured in the operating room at the time of palatoplasty. Results Fifty-seven patients without the PR sequence and 36 patients with the PR sequence were enrolled. Within the PR group, 61% of cases were mild and 39% were severe. A larger soft palate width was found to be statistically significant in a comparison of the severe PR cases with the isolated clefts (P < .005) and mild PR (P < .05), respectively. For the hard palate width, a statistically significant difference was found in a comparison of the narrower isolated cleft cases with the mild PR (P < .05) and the severe PR cases (P < .05), respectively. A shorter cleft length was found to be statistically significant in isolated clefts versus both the clefts of the mild PR (P < .05) and the severe PR cases (P < .05). Conclusions The patients with PR sequence presented statistically significant different cleft characteristics. The increased width of the cleft at the soft palate level showed the greatest correlation with increased airway and feeding problems.