Miracle-dz/UniFAR-FTUs huggingface dataset:
DeepSAGE Based Differential Gene Expression Analysis under Cold and Freeze Stress in Seabuckthorn (Hippophae rhamnoides L.)

Seabuckthorn (Hippophae rhamnoides L.), an important plant species of Indian Himalayas, is well known for its immense medicinal and nutritional value. The plant has the ability to sustain growth in harsh environments of extreme temperatures, drought and salinity. We employed DeepSAGE, a tag based approach, to identify differentially expressed genes under cold and freeze stress in seabuckthorn. In total 36.2 million raw tags including 13.9 million distinct tags were generated using Illumina sequencing platform for three leaf tissue libraries including control (CON), cold stress (CS) and freeze stress (FS). After discarding low quality tags, 35.5 million clean tags including 7 million distinct clean tags were obtained. In all, 11922 differentially expressed genes (DEGs) including 6539 up regulated and 5383 down regulated genes were identified in three comparative setups i.e. CON vs CS, CON vs FS and CS vs FS. Gene ontology and KEGG pathway analysis were performed to assign gene ontology term to DEGs and ascertain their biological functions. DEGs were mapped back to our existing seabuckthorn transcriptome assembly comprising of 88,297 putative unigenes leading to the identification of 428 cold and freeze stress responsive genes. Expression of randomly selected 22 DEGs was validated using qRT-PCR that further supported our DeepSAGE results. The present study provided a comprehensive view of global gene expression profile of seabuckthorn under cold and freeze stresses. The DeepSAGE data could also serve as a valuable resource for further functional genomics studies aiming selection of candidate genes for development of abiotic stress tolerant transgenic plants.
Evaluation of the ability of people with intellectual disabilities to 'weigh up' information in two tests of financial reasoning.

BACKGROUND An assessment of mental capacity includes an evaluation of the ability to 'weigh up' information, but how to do this is uncertain. We have previously used a laboratory decision-making task, temporal discounting, which involves a trade-off between the value and the delay of expected rewards. Participants with intellectual disabilities (ID) showed very little evidence of 'weighing up' of information: only a third of participants showed consistent temporal discounting performance, and when present, consistent performance was usually impulsive; and the ability to perform consistently was more strongly related to executive functioning than to IQ. The aim of the present study was to replicate these observations and extend them to a more realistic financial decision-making task. METHODS We administered a temporal discounting task and a financial decision-making task, as well as tests of executive functioning and IQ, to 20 participants who attended day services for people with learning disabilities (mean Full-Scale IQ = 59), and to 10 staff members. RESULTS Performance in both decision-making tasks was related more strongly to executive functioning than to IQ. In both tasks, decisions by service users were made largely on the basis of a single item of information: there was very little evidence in either task that information from two sources was being 'weighed'. CONCLUSIONS The results suggest that difficulty in 'weighing up' information may be a general problem for people with ID, pointing to a need for psycho-educational remediation strategies to address this issue. The importance of executive functioning in decision-making by people with ID is not recognized in the legal test for mental capacity, which in practice includes a possibly irrelevant IQ criterion.
Large Deviation Multifractal Analysis of a Class of Additive Processes With Correlated Nonstationary Increments

We consider a family of stochastic processes built from infinite sums of independent positive random functions on \BBR+. Each of these functions increases linearly between two consecutive negative jumps, with the jump points following a Poisson point process on \BBR+. The motivation for studying these processes stems from the fact that they constitute simplified models for TCP traffic. Such processes bear some analogy with Lévy processes, but are more complex since their increments are neither stationary nor independent. In the work of Barral and Lévy Véhel, the Hausdorff multifractal spectrum of these processes was computed. We are interested here in their Large Deviation and Legendre multifractal spectra. These “statistical” spectra are seen to give, in this case, a richer information than the “geometrical” Hausdorff spectrum. In addition, our results provide a firm theoretical basis for the empirical discovery of the multifractal nature of TCP traffic.
Global Behavior of the Cauchy Problem for Some Critical Nonlinear Parabolic Equations

The paper deals with the following nonlinear parabolic problem: u_t- \lp u &=& \lambda \dfrac {u^{p-1}}{|x|^p} \quad x \in \ren, \, t > 0, \\ u(x,0) &=& u_0 (x) \ge 0, where 1 0 $. The existence or nonexistence (blow-up) of global solution is analyzed. Also the finite time extinction for solutions in the case 1 < p<2 in bounded and unbounded domains is studied. This behavior depends on the relationships between $ \lambda $, N, p and the integrability of u0 .
The Effects of Neonatal Isoflurane Exposure in Mice on Brain Cell Viability, Adult Behavior, Learning, and Memory

BACKGROUND: Volatile anesthetics, such as isoflurane, are widely used in infants and neonates. Neurodegeneration and neurocognitive impairment after exposure to isoflurane, midazolam, and nitrous oxide in neonatal rats have raised concerns regarding the safety of pediatric anesthesia. In neonatal mice, prolonged isoflurane exposure triggers hypoglycemia, which could be responsible for the neurocognitive impairment. We examined the effects of neonatal isoflurane exposure and blood glucose on brain cell viability, spontaneous locomotor activity, as well as spatial learning and memory in mice. METHODS: Seven-day-old mice were randomly assigned to 6 h of 1.5% isoflurane with or without injections of dextrose or normal saline, or to 6 h of room air without injections (no anesthesia). Arterial blood gases and glucose were measured. After 2 h, 18 h, or 11 wk postexposure, cellular viability was assessed in brain sections stained with Fluoro-Jade B, caspase 3, or NeuN. Nine weeks postexposure, spontaneous locomotor activity was assessed, and spatial learning and memory were evaluated in the Morris water maze using hidden and reduced platform trials. RESULTS: Apoptotic cellular degeneration increased in several brain regions early after isoflurane exposure, compared with no anesthesia. Despite neonatal cell loss, however, adult neuronal density was unaltered in two brain regions significantly affected by the neonatal degeneration. In adulthood, spontaneous locomotor activity and spatial learning and memory performance were similar in all groups, regardless of neonatal isoflurane exposure. Neonatal isoflurane exposure led to an 18% mortality, and transiently increased Paco2, lactate, and base deficit, and decreased blood glucose levels. However, hypoglycemia did not seem responsible for the neurodegeneration, as dextrose supplementation failed to prevent neuronal loss. CONCLUSIONS: Prolonged isoflurane exposure in neonatal mice led to increased immediate brain cell degeneration, however, no significant reductions in adult neuronal density or deficits in spontaneous locomotion, spatial learning, or memory function were observed.
Expression of mRNAs for telomeric repeat binding factor (TRF)-1 and TRF2 in atypical adenomatous hyperplasia and adenocarcinoma of the lung.

PURPOSE AND EXPERIMENTAL DESIGN It has been suggested that atypical adenomatous hyperplasia (AAH) may be a precursor of peripheral adenocarcinoma of the lung. Telomerase is a ribonucleoprotein enzyme that synthesizes telomeric DNA onto chromosomal ends. Its activity is thought to participate in the development of most human cancers. Telomere-specific DNA-binding proteins, such as telomeric repeat binding factor 1 and telomeric repeat binding factor 2, also control telomere length in a complex interplay with telomerase. Here we investigated the expressions of the mRNAs encoded by the TERF1 and TERF2 genes using in situ hybridization in surgically resected specimens [28 AAHs (11 lesions were interpreted as low-grade AAH, and 17 were interpreted as high-grade AAH) and 40 peripherally located bronchioloalveolar carcinoma (BAC). RESULTS A clear overexpression of these mRNAs was recognized in low- and high-grade AAH and BAC samples (as compared with normal tissues) using in situ hybridization and these mRNAs were detected in normal AAH and BAC samples using reverse transcription-PCR. The expressions of TERF1 and TERF2 mRNA detected by in situ hybridization were scored positive in 36% and 82% of low-grade AAH, 65% and 83% of high-grade AAH, and 88% and 88% of BAC, respectively. Statistically significant differences in TERF1 mRNA expression could be shown between low-grade AAH and BAC and between high-grade AAH and BAC. There was no statistical difference in the positive expressions of TERF2 mRNA among low-grade AAH, high-grade AAH, and BAC. CONCLUSIONS These results are consistent with (but are not enough to confirm) the idea that high-grade AAH is closely related to BAC.
Treatment and surveillance of advanced, metastatic iodine-resistant differentiated thyroid cancer

Purpose of review This review will focus on the management and treatment of metastatic thyroid cancer that is radioactive iodine refractory and review the new drugs and their mechanism of actions as well as their adverse events. Recent findings Until recently, there were no efficacious therapeutic modalities for these patients. With advancement in knowledge and research of the molecular aberrations and oncogenic mutations in thyroid cancer as well as further understanding the role of angiogenesis in tumor growth molecular pathogenesis, novel targeted therapies are available for these patients. Some of these drugs have successfully prolonged progression free survival and are now Food and Drug Administration approved. Additional agents are approved for the treatment of other types of cancers and are currently under investigation for differentiated thyroid cancer treatment. Summary Differentiated thyroid cancer (papillary and follicular) is the most common endocrine malignancy. It is generally known to have an excellent prognosis and patients are usually cured with the conventional primary treatments including surgery, radioactive iodine, and thyroid stimulating hormone suppression. A minor proportion of patients do not fully recover mainly because they develop radioactive iodine-resistant disease. These patients have few treatment options, which we aimed to describe here.
[Ureter-ureterotransversostomy. A method for supravesical urinary diversion with few complications].

A simple method of urinary diversion is described. It is very useful in reduced patients when other methods, e.g. ureterosigmoidostomy, ileal and colonic conduits are impossible. Up to now 14 patients were treated by transuretero-ureterostomy combined with a definitely nephrostoma. In all cases except one an optimal urinary diversion was attained.
Latch-Based Structure: A High Resolution and Self-Reference Technique for Hardware Trojan Detection

Hardware Trojan detection has been the subject of many studies in the realm of hardware security in the recent years. The effectiveness of current techniques proposed for Trojan detection is limited by some factors, process variation noise being a major one. This paper introduces latch-based structures as a self-reference detection technique which uses in-circuit path delays as golden reference models. By addressing process variation, these structures can achieve high accuracy in detection resolution. The proposed method is a complementary approach to current side-channel techniques to cover their poor performance in detecting small Trojans. Simulation results show that this technique can detect small Trojans at the scale of only one logical gate with 90 percent probability on average.
Complete recovery time after exhaustion in high-intensity work

This study was aimed to investigate complete recovery time (CRT) after exhaustion in high-intensity work. Twenty-four subjects were divided into two groups based on the cardiorespiratory capability index, which was measured in a maximum capacity test. Each subject then performed two cycling tests (at 60% and 70% maximum working capacity). The subject continued cycling until exhaustion in each test and then sat recovering until he/she no longer felt fatigue or until the oxygen uptake (VO2) and heart rate (HR) returned to their baselines, whichever was longer. The results indicated that HR required the longest time to recover and, consequently, HR data were adopted to set the CRT. The CRT was significantly correlated with the cardiorespiratory capability index and the relative workload indices: RVO2 and RHR. The RVO2 was the average elevation in VO2 during work from the resting level as a percentage of maximum VO2 reserve. The RHR's definition was similar to that of RVO2. Based on the obtained CRT-prediction model, the CRT for a high-cardiorespiratory-capability person was 20.8, 22.1, 23.4, and 24.7 min at 50%, 60%, 70%, and 80% RHR levels, respectively. These suggested CRT values should be increased by 10 min for a low-cardiorespiratory-capability person.
Ilk conditional deletion in adult animals increases cyclic GMP-dependent vasorelaxation.

AIMS Integrin-linked kinase (ILK) regulates proliferation, differentiation, cell adhesion, and motility in many cell types and has been related to cancer progression, fibrosis, and vascular diseases. We designed the present study to directly explore the effect of ILK deletion on the regulation of vascular tone through the soluble guanylate cyclase (sGC) /protein kinase G (PKG) pathway in healthy adult mice. METHODS AND RESULTS Experiments were carried out using a tamoxifen-inducible CRE-LOX system to conditionally delete the ILK gene in adult mice. Mice lacking ILK expression (cKO) presented increased vascular content and increased activity of sGC and PKG, resulting in a more intense vasodilatory response to a single dose of a nitric oxide (NO) donor [sodium nitroprusside (SNP)] or PKG agonist [8-bromoguanosine 3',5'-cyclic monophosphate sodium salt (8-Br)]. Five minutes after SNP or 8-Br administration the reduction in the systolic arterial pressure was enhanced in cKO mice (SNP WT: -7.4 ± 1.2 mmHG; SNP cKO: -14.0 ± 2.5; 8-Br WT: -2.9 ± 1.5 mmHG; 8-Br cKO: -10.0 ± 3.4 mmHG). ILK deletion restored the vascular response to SNP after chronic oral nitrite administration. In addition, ILK deletion also increased hypotensive SNP effect in angiotensin II-treated animals, suggesting a role for ILK in basal and pathological states. CONCLUSION Deletion of ILK in adult animals increased the vascular response to NO. These findings show, for the first time, a requirement for ILK in regulating sGC-PKG expression in vivo.
Change in parent and peer support across ages 9 to 15 yr and adolescent girls' physical activity.

PURPOSE To examine change in parent and peer support for girls' physical activity (PA) across ages 9 to 15 yr and assess if girls who remain active during adolescence are differentially exposed to support when compared with girls who do not remain active. METHODS Participants included 174 non-Hispanic white girls assessed at ages 9, 11, 13, and 15 yr. Parental modeling and logistic support for PA were assessed at all ages; peer support was assessed at ages 9, 11, and 13 yr. Minutes per day of moderate-to-vigorous PA (MVPA) was measured at ages 13 and 15 yr using 7-d accelerometry. Girls' body mass index and self-reported PA were measured at ages 9, 11, and 13 yr. Girls were classified as maintaining PA during adolescence if they recorded > or =30 min.d of MVPA at ages 13 and 15 yr. Patterns of change in parent/peer support and differences in exposure to support for girls who maintained PA and those who did not maintain PA were assessed using individual growth curve modeling. RESULTS A linear decline was observed in parental modeling. A curvilinear pattern of change was observed for parental logistic support and peer support. Although the rate of change varied by age, logistic support generally decreased, and peer support increased across time. Girls who maintained PA had parents who reported higher modeling of PA across time and stable levels of logistic support. In contrast, girls who did not maintain PA had parents who reported lower modeling and declines in logistic support. CONCLUSIONS Parental modeling of PA before adolescence and logistic support during adolescence could help girls establish early patterns of PA and social networks that facilitate maintained PA during adolescence.
CellsFactor-7 Signaling in Primary Human T 1 and Fibroblast Growth b with TGF-Expression a Promoter Links Lymphotoxin A Stimulation-Dependent Alternate Core

Lymphotoxin (LT)- a regulates many biologic activities, yet little is known of the regulation of its gene. In this study, the contribution to LTA transcriptional regulation of the region between the transcription and translation start sites (downstream segment) was investigated. The LTA downstream segment was found to be required for, and alone to be sufﬁcient for, maximal transcriptional activity in both T and B lymphocytes. The latter observation suggested that an alternate core promoter might be present in the downstream segment. Characterization of LTA mRNAs isolated from primary and from transformed human T cells under different stimulation conditions identiﬁed eight unique transcript variants (TVs), including one ( LTA TV8) that initiated within a polypyrimidine tract near the 3 9 end of the downstream segment. Further investigation determined that the LTA downstream segment alternate core promoter that produces the LTA TV8 transcript most likely consists of a stimulating protein 1 binding site and an initiator element and that factors involved in transcription initiation (stimulating protein 1, TFII-I, and RNA polymerase II) bind to this LTA region in vivo. Interestingly, the LTA downstream segment alternate core promoter was active only after speciﬁc cellular stimulation and was the major promoter used when human T cells were stimulated with TGF- b 1 and ﬁbroblast growth factor-7. Most importantly, this study provides evidence of a direct link for crosstalk between T cells and epithelial/stromal cells that has implications for LT signaling by T cells in the cooperative regulation of various processes typically associated with TGF- b R and ﬁbroblast growth factor-R2 signaling. The Journal of Immunology , 2013, 190: 4573–4584.
A Corpus and Model Integrating Multiword Expressions and Supersenses

This paper introduces a task of identifying and semantically classifying lexical expressions in running text. We investigate the online reviews genre, adding semantic supersense annotations to a 55,000 word English corpus that was previously annotated for multiword expressions. The noun and verb supersenses apply to full lexical expressions, whether single- or multiword. We then present a sequence tagging model that jointly infers lexical expressions and their supersenses. Results show that even with our relatively small training corpus in a noisy domain, the joint task can be performed to attain 70% class labeling F1.
Tool from ancient pharmacopoeia prevents vision loss.

PURPOSE Bear bile has been used in Asia for over 3,000 years to treat visual disorders, yet its therapeutic potential remains unexplored in Western vision research. The purpose of this study was to test whether treatment of mice undergoing retinal degeneration with tauroursodeoxycholic acid (TUDCA), a primary constituent of bear bile, alters the course of degeneration. METHODS Two retinal degeneration models were tested: the rd10 mouse, which has a point mutation in the gene encoding the beta subunit of rod phosphodiesterase, and light induced retinal damage (LIRD). For LIRD studies, albino Balb/C adult mice were subcutaneously injected with TUDCA (500 mg/kg body weight) or vehicle (0.15 M NaHCO(3)). Sixteen h later, each mouse received repeat injections. Half of each treatment group was then placed in bright light (10,000 lux) or dim light (200 lux) for seven h. At the end of exposure, animals were transferred to their regular housing. Electroretinograms (ERGs) were assessed 24 h later, mice sacrificed, eyes embedded in paraffin and sectioned, and retina sections assayed for morphology and apoptosis by TUNEL and anti-active caspase-3 immunoreactivity via fluorescent confocal microscopy. A subset of mice were sacrificed 8 and 15 days after exposure and retina sections analyzed for morphology and apoptosis. For rd10 studies, mice were injected subcutaneously with TUDCA or vehicle at postnatal (P) days 6, 9, 12, and 15. At p18, ERGs were recorded, mice were euthanized and eyes were harvested, fixed, and processed. Retinal sections were stained (toluidine blue), and retinal cell layers morphometrically analyzed by light microscopy. Consecutive sections were analyzed for apopotosis as above. RESULTS By every measure, TUDCA greatly slowed retinal degeneration in LIRD and rd10 mice. ERG a-wave and b-wave amplitudes were greater in mice treated with TUDCA compared to those treated with vehicle. Retinas of TUDCA-treated mice had thicker outer nuclear layers, more photoreceptor cells, and more fully-developed photoreceptor outer segments. Finally, TUDCA treatments dramatically suppressed signs of apoptosis in both models. CONCLUSIONS Systemic injection of TUDCA, a primary constituent of bear bile, profoundly suppressed apoptosis and preserved function and morphology of photoreceptor cells in two disparate mouse models of retinal degeneration. It may be that bear bile has endured so long in Asian pharmacopeias due to efficacy resulting from this anti-apoptotic and neuroprotective activity of TUDCA. These results also indicate that a systematic, clinical assessment of TUDCA may be warranted.
How Does Moxibustion Possibly Work?

“Acupmoxa” is a hybrid word of “acupuncture” and “moxibustion” that more closely resembles the Chinese ideograph for this treatment. People in Western countries are more familiar with acupuncture, while moxibustion is less popular, partially due to the paucity of scientific studies. Although the evidence-based efficacy of moxibustion needs to be further clarified, the mechanisms by which moxibustion may work include temperature-related and nontemperature-related ones. Local somatothermal stimulation (LSTS), one type of moxibustion, is achieved by application of a heat source to and above the acupoint. Such mild heat stimulation of the acupoint induces little skin damage, in contrast to the burning effect of moxibustion, but does provoke mild oxidative stress in the viscera. Thus, preconditioned LSTS at the peripheral acupoints LR 14 and PC 6 of animals is able to induce visceral HSP70 expression and to protect the liver and the heart against ischemia-reperfusion injury. Nontemperature-related mechanisms include smoke, herbs, and biophysical (far infrared) stimulation. We conclude that LSTS, a remote preconditioning method, has potential clinical usefulness. However, evidence-based efficacy and safety studies involving large-scaled clinical trials are needed in order that this approach will pass muster with Western scientists.