Miracle-dz/UniFAR-FTUs huggingface dataset:
Elevated Body Weight Gain During the Juvenile Period Alters Neuropeptide Y-Gonadotropin-Releasing Hormone Circuitry in Prepubertal Heifers1

ABSTRACT Increased body weight (BW) gain during the juvenile period leads to early maturation of the reproductive neuroendocrine system. We investigated whether a nutritional regimen that advances the onset of puberty leads to alterations in the hypothalamic neuropeptide Y (NPY) circuitry that are permissive for enhanced gonadotropin-releasing hormone (GnRH) secretion. It was hypothesized that NPY mRNA and NPY projections to GnRH and kisspeptin neurons are reduced in heifers that gain BW at an accelerated rate, compared with a lower one, during the juvenile period. Heifers were weaned at approximately 4 mo of age and fed diets to promote relatively low (0.5 kg/day; low gain [LG]) or high (1.0 kg/day; high gain [HG]) rates of BW gain until 8.5 mo of age. Heifers that gained BW at a higher rate exhibited greater circulating concentrations of leptin and reduced overall NPY expression in the arcuate nucleus. The proportion of GnRH neurons in close apposition to NPY fibers and the magnitude of NPY projections to GnRH neurons located in the mediobasal hypothalamus were reduced in HG heifers. However, no differences in NPY projections to kisspeptin neurons in the arcuate nucleus were detected between HG and LG heifers. Results indicate that a reduction in NPY innervation of GnRH neurons, particularly at the level of the mediobasal hypothalamus, occurs in response to elevated BW gain during the juvenile period. This functional plasticity may facilitate early onset of puberty in heifers.
Plant identification using new geometric features with standard data mining methods

Plant identification belongs to a specific application domain of data mining. Images of plant leaves are usually used as the main element to distinguish a plant from another. For proper identification, feature extraction is necessary. In the literature, most plant recognition systems use the features along with a classification method, which has been adapted or modified to face this type of application. In this paper, we propose three new geometric features that describe the vertical and horizontal symmetry of leaves. These features are simple to extract from images. According to the results of experiments, when these features are used in conjunction with other well-known geometric characteristics, the performance of classical classification methods is remarkably improved. To show the effectiveness of the proposal, we test seven classifiers with images of leaves publicly available on the Internet.
Expression of OCT4 Transcription Factor in Cutaneous Neoplasia

The OCT4 transcription factor is a marker of pluripotency and is present in embryonic stem cells, primordial germ cells, and several neoplasms including seminoma, dysgerminoma, and embryonal carcinoma. Recently, immunohistochemical expression of OCT4 protein has been described in the cells within the basal layer of normal human and canine epidermis. We have examined a series of basal cell carcinomas and adnexal tumors of related histiogenesis, in an effort to corroborate the above findings and to assess for expression of OCT4 protein in neoplasia of the infundibulo-apocrine-sebaceous unit. We analyzed OCT4 expression in 115 cutaneous specimens including 26 basal cell carcinomas, 12 benign follicular tumors (10 trichoepitheliomas and 2 trichoblastomas), 10 benign apocrine tumors, 12 sebaceous hyperplasia lesions, 10 sebaceous adenomas, 4 sebaceous carcinomas, 13 nevi sebacei of Jadassohn, 8 squamous cell carcinomas (including one spindle-cell squamous cell carcinoma), 8 compound melanocytic nevi, 5 Me¨rkel cell carcinomas, 3 pilar cysts, 1 scar, 2 nonspecific, mild superficial perivascular dermatitis specimens, and 1 nonscaring alopecia. All 115 specimens examined were negative for OCT4 expression as was adjacent or overlying epidermis and follicular epithelium including the bulge region. In contrast to previous studies, our data indicate that the OCT4 expression is not retained in cutaneous neoplasms derived from basal epidermis or related adnexal neoplasms, including lesions of the scalp.
hnRNP L and NF90 Interact with Hepatitis C Virus 5′-Terminal Untranslated RNA and Promote Efficient Replication

ABSTRACT The 5′-terminal sequence of the hepatitis C virus (HCV) positive-strand RNA genome is essential for viral replication. Critical host factors, including a miR-122/Ago2 complex and poly(rC)-binding protein 2 (PCBP2), associate with this RNA segment. We used a biotinylated RNA pulldown approach to isolate host factors binding to the HCV 5′ terminal 47 nucleotides and, in addition to Ago2 and PCBP2, identified several novel proteins, including IGF2BP1, hnRNP L, DHX9, ADAR1, and NF90 (ILF3). PCBP2, IGF2BP1, and hnRNP L bound single-stranded RNA, while DHX9, ADAR1, and NF90 bound a cognate double-stranded RNA bait. PCBP2, IGF2BP1, and hnRNP L binding were blocked by preannealing the single-stranded RNA bait with miR-122, indicating that they bind the RNA in competition with miR-122. However, IGF2BP1 binding was also inhibited by high concentrations of heparin, suggesting that it bound the bait nonspecifically. Among these proteins, small interfering RNA-mediated depletion of hnRNP L and NF90 significantly impaired viral replication and reduced infectious virus yields without substantially affecting HCV internal ribosome entry site-mediated translation. hnRNP L and NF90 were found to associate with HCV RNA in infected cells and to coimmunoprecipitate with NS5A in an RNA-dependent manner. Both also associate with detergent-resistant membranes where viral replication complexes reside. We conclude that hnRNP and NF90 are important host factors for HCV replication, at least in cultured cells, and may be present in the replication complex. IMPORTANCE Although HCV replication has been intensively studied in many laboratories, many aspects of the viral life cycle remain obscure. Here, we use a novel RNA pulldown strategy coupled with mass spectrometry to identify host cell proteins that interact functionally with regulatory RNA elements located at the extreme 5′ end of the positive-strand RNA genome. We identify two, primarily nuclear RNA-binding proteins, hnRNP L and NF90, with previously unrecognized proviral roles in HCV replication. The data presented add to current understanding of the replication cycle of this pathogenic human virus.
A simple, robust and controllable nano-structures fabrication technique using standard silicon wafers

We succeeded to realize nano-structures using standard {100} silicon wafers and anisotropic etching; this technique makes use of the low etching rate in TMAH of {111} planes or silicon, in comparison to {100} planes, to adjust the nanometric dimensions of the structures. No sub-micron lithography is required in this technique: it is compatible with normal UV photolithography. Neither complicated process steps are required: a succession of oxidation, oxide patterning and anisotropic etching only are needed. Nano-holes and nano-wires were made using this technique and possible applications of the structures are described for two BIO-MEMS projects.
Identification of a Stage-Specific Permissive In Vitro Culture Environment for Follicle Growth and Oocyte Development1

Abstract The availability of viable oocytes is the limiting factor in the development of new reproductive techniques. Many attempts have been made to grow immature oocytes in vitro during recent decades. Recently, a modified alginate-based three-dimensional culture system was designed to support the growth and maturation of multilayered secondary follicles. This system was able to produce oocytes that successfully completed meiosis, fertilization, and development to the blastocyst stage. Subsequent attempts to culture two-layered secondary follicles were unsuccessful under the original conditions. Herein, we investigated the effect of alginate consistency on two-layered follicle growth and oocyte developmental competence by encapsulating follicles into alginate scaffolds of various concentrations. Although there were no significant differences in survival rates, 0.25% and 0.5% alginate supported more rapid growth of follicles and antrum formation compared with 1.5% and 1.0% alginate after 8 days of culture. Alginate scaffold concentration also affected the proliferation and differentiation of somatic cells (theca and granulosa cells), measured in terms of morphological changes, steroid profiles (androstenedione, estradiol, and progesterone), and specific molecular markers (Fshr, Lhcgr, and Gja1). Theca cell proliferation and steroid production were hindered in follicles cultured in 1.5% alginate. In vitro fertilization and embryo culture revealed that oocytes obtained from 0.25% alginate retained the highest developmental competence. Overall, the present study showed that the alginate scaffold consistency affects folliculogenesis and oocyte development in vitro and that the alginate culture system can and should be tailored to maximally support follicle growth depending on the size and stage of the follicles selected for culture.
Clearance of the Janus kinase 2 (JAK2) V617F mutation after allogeneic stem cell transplantation in a patient with myelofibrosis with myeloid metaplasia

A patient with myelofibrosis with myeloid metaplasia displaying the V617F mutation of the JAK2 gene was given an allogeneic stem cell transplantation using a reduced‐intensity conditioning regimen. The patient engrafted, and as he became a chimera, the expression of the V617F mutation of the JAK2 gene decreased progressively until its disappearance. Accordingly, the concept of “molecular remission” of the myelofibrosis with myeloid metaplasia could be entertained and added to the categories of response to treatment which have been recently described. Am. J. Hematol. , 2007. © 2006 Wiley‐Liss, Inc.
Family problems among recently returned military veterans referred for a mental health evaluation.

CONTEXT Existing evidence suggests that military veterans with mental health disorders have poorer family functioning, although little research has focused on this topic. OBJECTIVE To test whether psychiatric symptoms are associated with family reintegration problems in recently returned military veterans. DESIGN Cross-sectional survey of a clinical population. Respondents who were referred to behavioral health evaluation from April 2006 through August 2007 were considered for the survey. SETTING Philadelphia Veterans Affairs Medical Center, Pa. PARTICIPANTS 199 military veterans who served in Iraq or Afghanistan after 2001 and were referred for behavioral health evaluation from primary care (mean age = 32.7 years, SD = 9.1). MAIN OUTCOME MEASURES Measures included the Mini-International Neuropsychiatric Interview for psychiatric diagnoses, the 9-item Patient Health Questionnaire for depression diagnosis and severity, and screening measures of alcohol abuse and illicit substance use. A measure of military family readjustment problems and a screening measure of domestic abuse were developed for this study. RESULTS Three fourths of the married/cohabiting veterans reported some type of family problem in the past week, such as feeling like a guest in their household (40.7%), reporting their children acting afraid or not being warm toward them (25.0%), or being unsure about their family role (37.2%). Among veterans with current or recently separated partners, 53.7% reported conflicts involving "shouting, pushing, or shoving," and 27.6% reported that this partner was "afraid of them. " Depression and posttraumatic stress disorder symptoms were both associated with higher rates of family reintegration problems. CONCLUSIONS Mental health problems may complicate veterans' readjustment and reintegration into family life. The findings suggest an opportunity to improve the treatment of psychiatric disorders by addressing family problems.
Context‐related representation of timing processes in monkey motor cortex

Precise timing is essential for motor performance, though the neuronal representation of time is unknown. To explore neuronal correlates of timing processes during movement preparation and execution, we compared the activities of neurons recorded in monkey motor cortex during the performance of two tasks requiring correct time estimation in different contextual situations. Despite the fact that both tasks had many common features (e.g. same movements, same time intervals to estimate), they involved different degrees of spatial and temporal uncertainty. Our findings indicate that time is indeed represented in neuronal activity of the motor cortex, albeit strongly dependent on context and not in an invariant manner as a distinct process per se.
Effect of sous vide processing on physicochemical, ultrastructural, microbial and sensory changes in vacuum packaged chicken sausages

The processing of sous vide chicken sausages was optimized under vacuum packaging condition and cooking at 100 ℃ for 30 min (SV30), 60 min (SV60) and 120 min (SV120) and compared with aerobically cooked control at 100 ℃ for 30 min. Sous vide processing of chicken sausages (SV30) produced higher (p < 0.05) cooking yield, Hunterlab a* values and sensory attributes without affecting proximate composition and shear force values relative to control. The sodium dodecyl sulphate-polyacrylamide gel electrophoresis and scanning electron microscopy results revealed no significant changes in protein quality and emulsion ultra-structure due to SV30 processing relative to control sausages. Sous vide processing of chicken sausages enriched with rosemary diterpene phenols retained the freshness and quality up to 120 days during storage at 4 ± 1 ℃ relative to control sausages that were spoiled on 20th day. Lipid oxidation and microbial growth remained below the spoilage levels for all the SV-processed sausages throughout the storage and addition of rosemary diterpene mixture at 0.02% v/w reduced the microbial growth and improved (p < 0.05) the sensory attributes. Our results demonstrate that sous vide processing minimizes lipid oxidation and microbial growth of chicken sausages with improved product quality and shelf-life at 4 ± 1 ℃.
Correlation between an In Vitro Invasion Assay and a Murine Model of Burkholderia cepacia Lung Infection

ABSTRACT Our understanding of the virulence of Burkholderia cepacia complex lung infections in cystic fibrosis patients is incomplete. There is a great deal of variability in the clinical course, from simple colonization to severe and often fatal necrotizing pneumonia, termed cepacia syndrome. Multiple subspecies (called genomovars) have been identified, and these genomovars may hold the key to understanding the variable pathogenicity. Thirty-one B. cepacia complex isolates belonging to five of the seven genomovars were examined by using a gentamicin protection assay of invasion with A549 cells. The level of epithelial cell invasion by B. cepacia in the A549 model was relatively low compared with the data obtained for other pathogens and was often variable from assay to assay. Thus, a statistical approach was used to determine invasiveness. When this model was used, one of four genomovar I strains (25%), three of eight genomovar II strains (37.5%), seven of nine genomovar III strains (77.8%), one of four genomovar IV strains (25%), and none of the four genomovar V strains examined were defined as invasive. All other strains were categorized as either noninvasive or indeterminate. Invasive, noninvasive, and indeterminate isolates belonging to genomovars II and III were subsequently tested for splenic invasion with the mouse agar bead model. Correlation between the models for six strains was demonstrated. Our results indicate that a statistical model used to determine invasiveness in an in vitro invasion assay can be used to predict in vivo invasiveness.
Long-term repercussions of a pulmonary rehabilitation program on the indices of anxiety, depression, quality of life and physical performance in patients with COPD.

OBJECTIVE To assess the 24-month effects of a pulmonary rehabilitation program (PRP) on anxiety, depression, quality of life and physical performance of COPD patients. METHODS Thirty patients with COPD (mean age, 60.8 +/- 10 years; 70% males) participated in a 12-week PRP, which included 24 physical exercise sessions, 24 respiratory rehabilitation sessions, 12 psychotherapy sessions and 3 educational sessions. All patients were evaluated at baseline (pre-PRP), at the end of the treatment (post-PRP) and two years later (current) by means of four instruments: the Beck Anxiety Inventory; the Beck Depression Inventory; Saint George's Respiratory Questionnaire; and the six-minute walk test (6MWT). RESULTS The comparison between the pre-PRP and post-PRP values revealed a significant decrease in the levels of anxiety (pre-PRP: 10.7 +/- 6.3; post-PRP: 5.5 +/- 4.4; p = 0.0005) and depression (pre-PRP: 11.7 +/- 6.8; post-PRP: 6.0 +/- 5.8; p = 0.001), as well as significant improvements in the distance covered on the 6MWT (pre-PRP: 428.6 +/- 75.0 m; post-PRP: 474.9 +/- 86.3 m; p = 0.03) and the quality of life index (pre-PRP: 51.0 +/- 15.9; post-PRP: 34.7 +/- 15.1; p = 0.0001). There were no statistically significant differences between the post-PRP and current evaluation values. CONCLUSIONS The benefits provided by the PRP in terms of the indices of anxiety, depression and quality of life, as well as the improved 6MWT performance, persisted throughout the 24-month study period.
Dynamic neural responses to cue‐reactivity paradigms in heroin‐dependent users: An fMRI study

Neuroimaging methods have been employed to study cue‐reactivity‐induced neural correlates in the human brain. However, very few studies have focused on characterizing the dynamic neural responses to the factorial interactions between the cues and the subjects. Fifteen right‐handed heroin‐dependent subjects and 12 age‐matched nondrug using subjects participated in this study. Cue‐reactivity paradigms were employed, while changes in blood oxygenation level‐dependent (BOLD) signals were acquired by functional MRI (fMRI). The fMRI datasets were analyzed with AFNI software and repeated two‐way ANOVA was employed for factorial analyses. Neural correlates of factorial interactions between cue‐factor and subject‐factor were identified in the regions of the ventral tegmental area (VTA), the left and right amygdala, the left and right fusiform cortex, and the precuneus in the mesocorticolimbic system, and in the superior frontal, dorsal lateral prefrontal, and orbitofrontal cortices in the prefrontal cortex system. The neural response patterns in the prefrontal systems are dynamic: decreased response to neutral‐cues and increased response to heroin‐cues. Further, heroin‐cue‐induced neural responses within the subregions in the PFC system are significantly intercorrelated. In conclusion, the cue‐reactivity paradigms significantly activated the dynamic neural activations in the prefrontal system. It is suggested that the dynamic response patterns in the PFC system characterize the impaired brain control functions in heroin‐dependent subjects. Hum Brain Mapp, 2009. © 2008 Wiley‐Liss, Inc.
Efficient inhibition of both syncytium‐inducing and non‐syncytium‐inducing wild‐type HIV‐1 by lamivudine in vivo

Objective:To determine the effect of lamivudine (3TC) on syncytium-inducing (SI) and non-SI (NSI) HIV-1 populations in vivo. Design:Responses in virus load and 3TC resistance in 40 3TC-treated subjects were analysed in relation to the presence or absence of SI HIV-1 variants. Methods:Peripheral blood samples were collected at regular intervals from 40 HIV-1-infected subjects during 3TC treatment. Virus isolates obtained at the start of treatment were typed for SI-capacity by coculture with MT-2 cells. Changes in levels of viral RNA in plasma were determined by quantitative reverse transcriptase PCR. The relative amount of wild-type and mutant virus at codon 184, associated with HIV resistance to 3TC, was determined using a primer-guided nucleotide incorporation assay after amplification of part of the reverse transcriptase gene. In five subjects the frequency of productively infected CD4+ cells with SI or NSI variants was determined in relation to codon 184 genotype. Results:Twenty-six subjects harboured only NSI variants at baseline, whereas 14 subjects also harboured SI variants. Although baseline plasma viral RNA load and CD4 cell counts were different between the two groups, no differences in the response to 3TC therapy were observed for these parameters. In-depth analysis of five subjects showed that the kinetics of virus load changes and emergence of 3TC resistance mutations were similar in plasma and cells, and comparable for the SI and NSI populations present in one individual. Conclusions:These data show that, in contrast to didanosine and zidovudine, the pressure exerted by 3TC is similar for SI and NSI M184 populations.
Iron Biomarkers in Plasma, HFE Genotypes, and the Risk for Colorectal Cancer in a Prospective Setting

BACKGROUND: High iron levels can increase the formation of noxious oxygen radicals, which are thought to promote carcinogenesis. OBJECTIVE: The aim of this prospective study was to determine whether iron biomarkers and HFE genotypes, which influence iron regulation, constitute risk factors for colorectal cancer. DESIGN: This is a prospective nested case-referent study. SETTINGS: The study was performed within the population-based Northern Sweden Health and Disease Study. PATIENTS: The study included 226 cases of colorectal cancer and 437 matched referents. MAIN OUTCOME MEASURES: Conditional regression analysis was performed. Adjustments for smoking, smoking and BMI, and HFE C282Y and H63D were performed. RESULTS: The highest quintile of total iron-binding capacity showed significantly higher risk for colorectal cancer, unadjusted OR 2.35 (95% CI 1.38–4.02). When stratified by sex, the findings were only present in women (OR 3.34 (95% CI 1.59–7.02)). Ferritin was associated with reduced risk throughout quintiles 2 to 5 both in univariate and multivariate models. LIMITATIONS: Colorectal cancer may influence iron markers because of occult bleeding. Homozygotes for HFE C282Y were too few to make conclusions for this group. The relatively short follow-up time might be insufficient to detect risk of iron biomarkers. CONCLUSIONS: High iron levels do not increase the risk of colorectal cancer. HFE genotypes influencing iron uptake had no effect on colorectal cancer risk.
Integration of UML and B specification techniques: systematic transformation from OCL expressions into B

In the continuity of our research on integration of UML and B, we address the transformation from OCL (Object Constraint Language), which is an integral part of UML, into B. Our derivation schemes allow to systematically even automatically derive into B not only the complementary class invariants, the statechart guard conditions, but also the OCL specification for UML operations.