Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiological, Behavioral, and Life-History Adaptations to Environmental Fluctuations in the Edible Dormouse

The edible dormouse (Glis glis, formerly Myoxus glis) is a small arboreal mammal inhabiting deciduous forests in Europe. This rodent shows behavioral and physiological adaptations to three types of environmental fluctuations: (i) predictable seasonal variation in climate and food resources (ii) unpredictable year-to-year fluctuation in seed-production by trees and (iii) day-to-day variation in ambient temperature and precipitation. They cope with seasonally fluctuating conditions by seasonal fattening and hibernation. Dormice have adjusted to tree-mast fluctuations, i.e., pulsed resources, by sensing future seed availability in spring, and restricting reproduction to years with at least some seed production by beech and oak trees, which are a crucial food-resource for fast-growing juveniles in fall. Finally, dormice respond to short-term drops in ambient temperature by increased use of daily torpor as well as by huddling in groups of up to 24 conspecifics. These responses to environmental fluctuations strongly interact with each other: Dormice are much more prone to using daily torpor and huddling in non-reproductive years, because active gonads can counteract torpor and energy requirements for reproduction may prevent the sharing of food resources associated with huddling. Accordingly, foraging activity in fall is much more intense in reproductive mast years. Also, depending on their energy reserves, dormice may retreat to underground burrows in the summers of non-reproductive years, causing an extension of the hibernation season to up to 11.4 months. In addition to these interactions, responses to environmental fluctuations are modulated by the progression of life-history stages. With increasing age and diminishing chances of future reproduction, females reproduce with increasing frequency even under suboptimal environmental conditions. Simultaneously, older dormice shorten the hibernation season and phase-advance the emergence from hibernation in spring, apparently to occupy good breeding territories early, despite increased predation risk above ground. All of the above adaptions, i.e., huddling, torpor, hibernation, and reproduction skipping do not merely optimize energy-budgets but also help to balance individual predation risk against reproductive success, which adds another layer of complexity to the ability to make flexible adjustments in this species.
Ultrastructural Study of West Nile Virus Pathogenesis in Culex pipiens quinquefasciatus (Diptera: Culicidae)

Abstract The ultrastructural features of West Nile virus (WNV) replication and dissemination in orally infected Culex pipiens quinquefasciatus Say were analyzed over a 25-d infection period. To investigate the effects of virus replication on membrane induction, cellular organization, and cell viability in midgut and salivary gland tissues, midguts were dissected on days 3, 7, 14, and 21, and salivary glands were collected on days 7, 14, 21, and 25 postinfection (d.p.i.) for examination by transmission electron microscopy (TEM). Whole mosquito heads were embedded for TEM analysis 14 d.p.i. to localize WNV particles and to investigate the effects of replication on nervous tissues of the brain. Membrane proliferation was induced by WNV in the midgut epithelium, midgut muscles, and salivary glands, although extensive endoplasmic reticulum swelling was a unique feature of salivary gland infection. TEM revealed WNV-induced pathology in salivary glands at 14, 21, and 25 d.p.i. , and we hypothesize that long-term virus infection of this tissue results in severe cellular degeneration and apoptotic-like cell death. This finding indicates that the efficiency of WNV transmission may decrease with mosquito age postinfection.
Econometric Models for Mixed-Frequency Data

Defence date: 7 September 2012; Examining Board: Professor Massimiliano Marcellino, EUI, Supervisor; Professor Tommaso di Fonzo, Universita di Padova; Professor Eric Ghysels, University of North Carolina; Professor Helmut Lutkepohl, Humboldt University Berlin
Comparative (Within Species) Genomics of the Vitis vinifera L. Terpene Synthase Family to Explore the Impact of Genotypic Variation Using Phased Diploid Genomes

The Vitis vinifera L. terpene synthase (VviTPS) family was comprehensively annotated on the phased diploid genomes of three closely related cultivars: Cabernet Sauvignon, Carménère and Chardonnay. VviTPS gene regions were grouped to chromosomes, with the haplotig assemblies used to identify allelic variants. Functional predictions of the VviTPS subfamilies were performed using enzyme active site phylogenies resulting in the putative identification of the initial substrate and cyclization mechanism of VviTPS enzymes. Subsequent groupings into conserved catalytic mechanisms was coupled with an analysis of cultivar-specific gene duplications, resulting in the identification of conserved and unique VviTPS clusters. These findings are presented as a collection of interactive networks where any VviTPS of interest can be queried through BLAST, allowing for a rapid identification of VviTPS-subfamily, enzyme mechanism and degree of connectivity (i.e., extent of duplication). The comparative genomic analyses presented expands our understanding of the VviTPS family and provides numerous new gene models from three diploid genomes.
Distribution of pesticide residues in soil and uncertainty of sampling

ABSTRACT Pesticide residues were determined in about 120 soil cores taken randomly from the top 15 cm layer of two sunflower fields about 30 days after preemergence herbicide treatments. Samples were extracted with acetone-ethyl acetate mixture and the residues were determined with GC-TSD. Residues of dimethenamid, pendimethalin, and prometryn ranged from 0.005 to 2.97 mg/kg. Their relative standard deviations (CV) were between 0.66 and 1.13. The relative frequency distributions of residues in soil cores were very similar to those observed in root and tuber vegetables grown in pesticide treated soils. Based on all available information, a typical CV of 1.00 was estimated for pesticide residues in primary soil samples (soil cores). The corresponding expectable relative uncertainty of sampling is 20% when composite samples of size 25 are taken. To obtain a reliable estimate of the average residues in the top 15 cm layer of soil of a field up to 8 independent replicate random samples should be taken. To obtain better estimate of the actual residue level of the sampled filed would be marginal if larger number of samples were taken.
VCA nanobodies target N-WASp to reduce invadopodium formation and functioning

Invasive cancer cells develop small actin-based protrusions called invadopodia, which perform a primordial role in metastasis and extracellular matrix remodelling. Neural Wiskott-Aldrich syndrome protein (N-WASp) is a scaffold protein which can directly bind to actin monomers and Arp2/3 and is a crucial player in the formation of an invadopodium precursor. Expression modulation has pointed to an important role for N-WASp in invadopodium formation but the role of its C-terminal VCA domain in this process remains unknown. In this study, we generated alpaca nanobodies against the N-WASp VCA domain and investigated if these nanobodies affect invadopodium formation. By using this approach, we were able to study functions of a selected functional/structural N-WASp protein domain in living cells, without requiring overexpression, dominant negative mutants or siRNAs which target the gene, and hence the entire protein. When expressed as intrabodies, the VCA nanobodies significantly reduced invadopodium formation in both MDA-MB-231 breast cancer and HNSCC61 head and neck squamous cancer cells. Furthermore, expression of distinct VCA Nbs (VCA Nb7 and VCA Nb14) in PC-3 prostate cancer cells resulted in reduced overall matrix degradation without affecting MMP9 secretion/activation or MT1-MMP localisation at invadopodial membranes. From these results, we conclude that we have generated nanobodies targeting N-WASp which reduce invadopodium formation and functioning, most likely via regulation of N-WASp—Arp2/3 complex interaction, indicating that this region of N-WASp plays an important role in these processes.
Adjuvant role of radiation therapy for locally advanced laryngeal cancer without pathological lymph node metastasis

Abstract Conclusion The application of adjuvant RT to reduce recurrence should be tailored in cases of pathologically negative node metastasis. Objectives The treatment modality following surgical resection of advanced laryngeal cancer is determined by adverse factors. Aside from lymph node metastasis (LNM) or positive margins, definite risk factors supporting adjuvant radiation therapy (RT) have not been clearly suggested. The aim of this study was to analyze the risk factors for advanced laryngeal cancer without LNM and the role of RT. Materials and methods Pathologically T3 and T4-staged laryngeal squamous cell carcinoma without LNM were reviewed. The patients were classified into RT (+) (n = 22) and RT (−) (n = 38) groups. Results Five-year overall survival (OS) of the RT (+) and RT (−) groups was 84.4% and 83.8%, respectively. Five-year disease-specific survival of the RT (+) and RT (−) groups was 88.4% and 93.9%. Five-year local control rate of the RT (+) and RT (−) groups was 94.7% and 91.3%. The factors affecting OS were smoking history and recurrence history (p = 0.02). By multivariate analysis, smoking history and recurrence history were determining factors for 5-year OS (p = 0.024 and p = 0.047, respectively).
Plexiform angiomyxoid myofibroblastic tumour: differential diagnosis of gastrointestinal stromal tumour in the stomach

Mesenchymal tumours other than gastrointestinal stromal tumours are rare in the stomach. Nevertheless it is important to incorporate them into the differential diagnosis. Plexiform angiomyxoid myofibroblastic tumour is a recently described new entity of a presumably benign mesenchymal gastric tumour. This report presents what is believed to be the third case of this tumour. The tumour is characterised by bland spindle cells in a plexiform pattern, a mucinous extracellular matrix and a network of thin blood vessels. These findings are completely in line with the two previous reported cases. There was a strong positivity for α-smooth muscle actin and a low proliferation index (<2%). The tumour had no C-KIT or CD34 expression and no mutation in the C-KIT and PDFGRα genes. Plexiform angiomyxoid myofibroblastic tumour may present a new mesenchymal tumour entity in the stomach.
Tactile innervation densities across the whole body

The skin is our largest sensory organ and innervated by afferent fibers carrying tactile information to the spinal cord and onto the brain. The density with which different classes of tactile afferents innervate the skin is not constant but varies considerably across different body regions. However, precise estimates of innervation density are only available for some body parts, such as the hands, and estimates of the total number of tactile afferent fibers are inconsistent and incomplete. Here we reconcile different estimates and provide plausible ranges and best estimates for the number of different tactile fiber types innervating different regions of the skin, using evidence from dorsal root fiber counts, microneurography, histology, and psychophysics. We estimate that the skin across the whole body is innervated by approximately 230,000 tactile afferent fibers (plausible range: 200,000-270,000). 15% innervate the palmar skin of both hands and 19% the region surrounding the face and lips. Around 60% of all tactile fibers are slowly-adapting, while the rest are fastadapting. Innervation density correlates well with psychophysical spatial acuity across different body regions, and additionally, on hairy skin, with hair follicle density. Innervation density is also weakly correlated with the size of the cortical somatotopic representation, but cannot fully account for the magnification of the hands and the face.
Fyn is a novel target of (−)‐epigallocatechin gallate in the inhibition of JB6 Cl41 cell transformation

The cancer preventive action of (−)‐epigallocatechin gallate (EGCG), found in green tea, is strongly supported by epidemiology and laboratory research data. However, the mechanism by which EGCG inhibits carcinogenesis and cell transformation is not clear. In this study, we report that EGCG suppressed epidermal growth factor (EGF)‐induced cell transformation in JB6 cells. We also found that EGCG inhibited EGF‐induced Fyn kinase activity and phosphorylation in vitro and in vivo. Fyn was implicated in the process because EGF‐induced JB6 cell transformation was inhibited by small interfering RNA (siRNA)‐Fyn‐JB6 cells. With an in vitro protein‐binding assay, we found that EGCG directly bound with the GST‐Fyn‐SH2 domain but not the GST‐Fyn‐SH3 domain. The Kd value for EGCG binding to the Fyn SH2 domain was 0.367 ± 0.122 µM and Bmax was 1.35 ± 0.128 nmol/mg. Compared with control JB6 Cl41 cells, EGF‐induced phosphorylation of p38 MAP kinase (p38 MAPK) (Thr180/Tyr182), ATF‐2 (Thr71) and signal transducer and activator of transcription 1 (STAT1) (Thr727) was decreased in siRNA‐Fyn‐JB6 cells. EGCG could inhibit the phosphorylation of p38 MAPK, ATF‐2, and STAT1. The DNA binding ability of AP‐1, STAT1, and ATF‐2 was also decreased in siRNA‐Fyn‐JB6 cells. Overall, these results demonstrated that EGCG interacted with Fyn and inhibited Fyn kinase activity and thereby regulated EGF‐induced cell transformation. Inhibition of Fyn kinase activity is a novel and important mechanism that may be involved in EGCG‐induced inhibition of cell transformation. © 2007 Wiley‐Liss, Inc.
Detection of Early Diabetic Change with Optical Coherence Tomography in Type 2 Diabetes Mellitus Patients without Retinopathy

Purpose: To detect early diabetic damage in type 2 diabetes mellitus patients with no diabetic retinopathy (NDR) using optical coherence tomography (OCT) and to evaluate OCT as a clinical test. Methods: Thirty-two patients with NDR (n = 32) were enrolled. We examined retinal and retinal nerve fiber layer (RNFL) thickness using OCT. Two healthy normal populations were also enrolled for the retinal thickness (n = 48) and RNFL thickness (n = 34). Both OCT measurements were obtained in four areas (temporal, superior, nasal and inferior). The receiver operator characteristic (ROC) curve was generated to evaluate the predictor variables. Results: Comparing the normal and NDR eyes, retinal thickness significantly increased (p = 0.03) and RNFL thickness significantly decreased (p = 0.02) in the superior areas. The area under the ROC curve was 0.65 for the superior retinal thickness and 0.63 for the superior RNFL thickness. Conclusions: Both OCT measurements can detect early retinal damage in NDR patients.
A Goal Unrealized: Patient Empowerment on Hand Hygiene- A Web-Based Survey from India.

INTRODUCTION Each year, millions of patients around the world are affected by Health Care Associated Infections (HCAIs). Understanding and assessing the global burden of HCAI is one of the key areas of work to improve the hand hygiene. AIM To assess the patient empowerment and awareness on hand hygiene among online users. MATERIALS AND METHODS A web-based cross-sectional survey was conducted during September 2013 to December 2013 among adults. A predesigned questionnaire to assess the awareness on hand hygiene was sent to volunteers through emails and social networking sites. The data were transferred to excel sheet and analyzed in Epi info and represented in proportions and percentages. RESULTS Total 94 (57%) participants responded to the survey among which 51.1% were males and 48.9% were females. Majority of them belongs to the age group of 20 to 35 years. Only 28.7% of them said they will ever ask health care worker to wash their hands before they examine. A 27.7% of the participants reported that their country/community have a program that educates/communicates with patients about the importance of hand hygiene. CONCLUSION Adherence and compliance to hand hygiene practices is suboptimal among people. There seems to be a lack of knowledge regarding hand hygiene.
Effectiveness of psychotherapeutic treatment of personality disorder

Background Psychiatrists have been criticised for failing to develop adequate treatment for personality disorder. Psychotherapeutic treatments are promising, but their effectiveness is uncertain. Aims To investigate the evidence for effectiveness of psychotherapeutic treatment for personality disorder. Method Systematic literature review. Results There is evidence for the effectiveness of psychotherapy for personality disorder. Problems of case identification, comorbidity, randomisation, specificity of treatment and outcome measurement are inadequately addressed. Authors mainly relied on cohort studies. Evidence neither suggests superiority of one type of therapy over another nor indicates which subgroups of patients should be offered psychotherapy as in-patient, day patient, or out-patient. Conclusions New research strategies are needed to show that personality change is both measurable and clinically meaningful. Effectiveness studies using randomised controlled designs are required. The literature suggests that effective treatment should be long-term, integrated, theoretically coherent and focused on compliance.
LOC387715/HTRA1 gene polymorphisms and susceptibility to age-related macular degeneration: A HuGE review and meta-analysis

Purpose To examine the association of age-related macular degeneration (AMD) with HtrA serine peptidase 1 (HTRA1) gene rs11200638 G→A polymorphism and LOC387715/ ARMS2 gene rs10490924 G→T polymorphisms, and to evaluate the magnitude of the gene effect and the possible genetic mode of action. Methods We searched the US National Library of Medicine’s PubMed, Embase, OMIM, ISI Web of Science, and CNKI databases in a systematic manner to retrieve all genetic association studies on the HTRA1 (rs11200638) and LOC387715/ ARMS2 (rs10490924) gene polymorphisms and AMD. We performed a meta-analysis conducted with Stata software, version 9.0. Results Individuals who carried the AA and AG genotypes of HTRA1 gene rs11200638 G→A polymorphism had 2.243 and 8.669 times the risk of developing AMD, respectively, when compared with those who carry the GG genotype. Individuals carrying the TT and TG genotypes of LOC387715/ ARMS2 gene rs10490924 G→T polymorphism had 7.512 and 2.353 times the risk of developing AMD, respectively, compared with those who carry GG genotype. These results suggested a “moderate” codominant, multiplicative genetic mode; that is, both HTRA1 rs11200638 G→A polymorphism and LOC387715/ARMS2 rs10490924 G→T polymorphism play important roles in the pathogenesis of AMD. We found no evidence of publication bias. Between-study heterogeneity was found in both allele-based analysis and genotype-based analysis. Conclusions HTRA1 rs11200638 G→A polymorphism and LOC387715/ARMS2 rs10490924 G→T polymorphism play important roles in AMD. Gene-gene and gene-environmental interactions, as well as precise mechanisms underlying common variants in the HTRA1 gene and LOC387715/ ARMS2 gene, potentially increase the risk of AMD and need further exploration.
The Accessory Factor Nef Links HIV-1 to Tec/Btk Kinases in an Src Homology 3 Domain-dependent Manner*♦

Background: HIV-1 replication in T cells requires the activity of the Tec family kinase Itk. Results: Cell-based fluorescence complementation shows that HIV-1 Nef selectively interacts with Itk, Btk, and Bmx through their SH3 domains. Conclusion: Nef links HIV-1 with the host cell kinase Itk during the viral life cycle. Significance: Selective inhibition of Nef-Itk signaling may be of therapeutic benefit in HIV/AIDS. The HIV-1 Nef virulence factor interacts with multiple host cell-signaling proteins. Nef binds to the Src homology 3 domains of Src family kinases, resulting in kinase activation important for viral infectivity, replication, and MHC-I down-regulation. Itk and other Tec family kinases are also present in HIV target cells, and Itk has been linked to HIV-1 infectivity and replication. However, the molecular mechanism linking Itk to HIV-1 is unknown. In this study, we explored the interaction of Nef with Tec family kinases using a cell-based bimolecular fluorescence complementation assay. In this approach, interaction of Nef with a partner kinase juxtaposes nonfluorescent YFP fragments fused to the C terminus of each protein, resulting in YFP complementation and a bright fluorescent signal. Using bimolecular fluorescence complementation, we observed that Nef interacts with the Tec family members Bmx, Btk, and Itk but not Tec or Txk. Interaction with Nef occurs through the kinase Src homology 3 domains and localizes to the plasma membrane. Allelic variants of Nef from all major HIV-1 subtypes interacted strongly with Itk in this assay, demonstrating the highly conserved nature of this interaction. A selective small molecule inhibitor of Itk kinase activity (BMS-509744) potently blocked wild-type HIV-1 infectivity and replication, but not that of a Nef-defective mutant. Nef induced constitutive Itk activation in transfected cells that was sensitive to inhibitor treatment. Taken together, these results provide the first evidence that Nef interacts with cytoplasmic tyrosine kinases of the Tec family and suggest that Nef provides a mechanistic link between HIV-1 and Itk signaling in the viral life cycle.
Hand and body position during locomotor behavior in the aye‐aye (Daubentonia madagascariensis)

Aye‐ayes (Daubentonia madagascariensis) have unique hands among primates, with extraordinarily long fingers in relation to body size. These long digits may be vulnerable to damage from forces during locomotion, particularly during head‐first descent—a locomotor mode that the aye‐aye utilizes frequently. Previous behavioral studies of aye‐aye locomotion reported that Daubentonia must curl its fingers during horizontal quadrupedalism and/or descent to reduce potential stresses on its long fingers. To test this hypothesis, we examined hand and body position in three captive adult aye‐ayes while they walked quadrupedally on horizontal and oblique branches. Substantial variation in hand position was observed among individuals for each substrate orientation. While hand postures with curled fingers were preferred by one individual during descent, they were not preferred by the other two individuals, contrary to our expectations. Differences in body position were more consistent among all three individuals. The angle of the body relative to the substrate was significantly reduced during descent (8.4°) compared to horizontal locomotion (16.9°). These results suggest that changes in body position, rather than hand position, may help reduce stresses on the digits. A biomechanical model is proposed that demonstrates how a reduction in the body angle in relation to substrate may act to move the center of mass more caudally. This mechanism of moderating loads by altering body position, rather than hand position, may represent an important functional aspect of arboreal locomotion in aye‐ayes and other primates. © 2002 Wiley‐Liss, Inc.