Miracle-dz/UniFAR-FTUs huggingface dataset:
GeoChip 4: a functional gene‐array‐based high‐throughput environmental technology for microbial community analysis

Micro‐organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro‐organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro‐organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long‐term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long‐term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.
The Facts behind the Figures: The Validation of The Older Persons and Informal Caregivers Minimum Data Set

Introduction: In 2008, the Ministry of Health, Welfare and Sport commissioned the National Care for the Elderly Programme. While numerous research projects in older persons’ health care were to be conducted under this national agenda, the Programme further advocated the development of The Older Persons and Informal Caregivers Survey Minimum DataSet (TOPICS-MDS) which would be integrated into all funded research protocols. In this context, we describe TOPICS data sharing initiative (www.topics-mds.eu). Materials and methods: A working group drafted TOPICS-MDS prototype, which was subsequently approved by a multidisciplinary panel. Using instruments validated for older populations, information was collected on demographics, morbidity, quality of life, functional limitations, mental health, social functioning and health service utilisation. For informal caregivers, information was collected on demographics, hours of informal care and quality of life (including subjective care-related burden). Results: Between 2010 and 2013, a total of 41 research projects contributed data to TOPICS-MDS, resulting in preliminary data available for 32,310 older persons and 3,940 informal caregivers. The majority of studies sampled were from primary care settings and inclusion criteria differed across studies. Discussion: TOPICS-MDS is a public data repository which contains essential data to better understand health challenges experienced by older persons and informal caregivers. Such findings are relevant for countries where increasing health-related expenditure has necessitated the evaluation of contemporary health care delivery. Although open sharing of data can be difficult to achieve in practice, proactively addressing issues of data protection, conflicting data analysis requests and funding limitations during TOPICS-MDS developmental phase has fostered a data sharing culture. To date, TOPICS-MDS has been successfully incorporated into 41 research projects, thus supporting the feasibility of constructing a large (>30,000 observations), standardised dataset pooled from various study protocols with different sampling frameworks. This unique implementation strategy improves efficiency and facilitates individual-level data meta-analysis.
Promoting Employer Practices That Increase Retention And Advancement

The implementation of welfare reform and the Workforce Investment Act and has helped thousands of low-income individuals join the workforce. However, many welfare leavers obtain jobs with low wages, lack of health benefits, and few opportunities for career advancement. As a result, helping those with jobs to stay employed and attain a family-supporting wage remains a key challenge for public agencies.
Probiotics and antibodies to TNF inhibit inflammatory activity and improve nonalcoholic fatty liver disease

Ob/ob mice, a model for nonalcoholic fatty liver disease (NAFLD), develop intestinal bacterial overgrowth and overexpress tumor necrosis factor α (TNF‐α). In animal models for alcoholic fatty liver disease (AFLD), decontaminating the intestine or inhibiting TNF‐α improves AFLD. Because AFLD and NAFLD may have a similar pathogenesis, treatment with a probiotic (to modify the intestinal flora) or anti‐TNF antibodies (to inhibit TNF‐α activity) may improve NAFLD in ob/ob mice. To evaluate this hypothesis, 48 ob/ob mice were given either a high‐fat diet alone (ob/ob controls) or the same diet + VSL#3 probiotic or anti‐TNF antibodies for 4 weeks. Twelve lean littermates fed a high‐fat diet served as controls. Treatment with VSL#3 or anti‐TNF antibodies improved liver histology, reduced hepatic total fatty acid content, and decreased serum alanine aminotransferase (ALT) levels. These benefits were associated with decreased hepatic expression of TNF‐α messenger RNA (mRNA) in mice treated with anti‐TNF antibodies but not in mice treated with VSL#3. Nevertheless, both treatments reduced activity of Jun N‐terminal kinase (JNK), a TNF‐regulated kinase that promotes insulin resistance, and decreased the DNA binding activity of nuclear factor κB (NF‐κB), the target of IKKβ, another TNF‐regulated enzyme that causes insulin resistance. Consistent with treatment‐related improvements in hepatic insulin resistance, fatty acid β‐oxidation and uncoupling protein (UCP)‐2 expression decreased after treatment with VSL#3 or anti‐TNF antibodies. In conclusion, these results support the concept that intestinal bacteria induce endogenous signals that play a pathogenic role in hepatic insulin resistance and NAFLD and suggest novel therapies for these common conditions.
Understanding Brand Implication and Engagement on Facebook

What are the drivers for Brand engagement and implication on Facebook? In order to explore the impact of motivations on content and information sharing on Facebook brand pages, this study proposes an analysis focused on a reduced number of motivations and a proposal of a statistical model attempting to link the frequency of posting and liking on Facebook in general and Brand engagement to motivations. The aim of the study is to assess the impact of motivations on brand implication and frequency of posting on Facebook. The authors use the concept of brand implication measure a deep interest toward brands on Facebook. The concept of frequency of posting and liking focuses on the tendency to post or like frequently each time the user connects to Facebook. The motivations the authors introduced are based on the literature for sharing on social networks.
Performance Implications and Fit of Knowledge Management Strategy and Strategic Information Technology Management

Fit issues in the Information System (IS) field have become a justifiable area. A number of theoretical frameworks have proposed to develop the linkages between IS/IT (Information Technology) and a firm’s related strategies. However, while there has been much theorizing in the area, validated empirical studies for using fit perspective in KM (Knowledge Management) topics have been scarce. Therefore, this present study empirically examines the KM performance implications of fit between KM strategy with its Strategic IT Management (SITM). Valid respondents from 161 organizations in Taiwan completed the questionnaires. A structural equation-modeling tool with second order factor viewed fit was used to examine the research model. Drawing on a covariation perspective of fit, the result of this study show that KM performance is significantly resulted from the well fit between KM strategy and strategic IT management. Yue-Yang Chen I-Shou University, Taiwan
Characterization and engineering of sequences controlling in vivo synthesis of brome mosaic virus subgenomic RNA

Expression of brome mosaic virus (BMV) coat protein and internal genes of many other positive-strand RNA viruses requires initiation of subgenomic mRNA synthesis from specific internal sites on minus-strand genomic RNA templates. Biologically active viral cDNA clones were used to investigate the sequences controlling production of BMV subgenomic RNA in vivo. Suitable duplications directed production of specifically initiated, capped subgenomic RNAs from new sites in the BMV genome. Previously implicated promoter sequences extending 20 bases upstream (-20) and 16 bases downstream (+16) of the subgenomic RNA initiation site directed only low-level synthesis. Subgenomic RNA production at normal levels required sequences extending to at least -74 but not beyond -95. Loss of an (rA)18 tract immediately upstream of the -20 to +16 "core promoter" particularly inhibited subgenomic RNA synthesis. The -38 to -95 region required for normal initiation levels contains repeats of sequence elements in the core promoter, and duplications creating additional upstream copies of these repeats stimulated subgenomic RNA synthesis above wild-type levels. At least four different subgenomic RNAs can be produced from a single BMV RNA3 derivative. For all derivatives producing more than one subgenomic RNA, a gradient of accumulation progressively favoring smaller subgenomic RNAs was seen.
Characterization of a power line cable for channel frequency response — Analysis and investigation

This paper focuses on the determination of the Channel Frequency Response (CFR) for a length of power cable which is crucial in determining the channel performance. The per-unit-length (PUL) parameters of a power line cable is used to calculate the CFR theoretically. This is verified by real world measurement. A new approach is introduced to model the PUL parameters. This work focus on characterizing a 1.5mm2 twin and earth (ribbon), 10-meter length cable. PUL parameters are estimated from measurements using an impedance analyzer. Further, the corresponding channel frequency response (CFR) is calculated using the developed equation. The accuracy of this investigation is being tested with a frequency range from 1 to 100 MHz. Numerical simulation results provided in this paper are in close agreement with the theoretical aspects of the CFR.
Stoichiometric and nutrient resorption characteristics of dominant tree species in subtropical Chinese forests

Abstract This study investigated seasonal patterns in stoichiometric ratios, nutrient resorption characteristics, and nutrient use strategies of dominant tree species at three successional stages in subtropical China, which have not been fully understood. Fresh leaf and leaf litterfall samples were collected in growing and nongrowing seasons for determining the concentrations of carbon (C), nitrogen (N), and phosphorus (P). Then, stoichiometric ratios (i.e., C:N, C:P, N:P, and C:N:P) and resorption parameters were calculated. Our results found that there was no consistent variation in leaf C:N and C:P ratios among different species. However, leaf N:P ratios in late‐successional species became significantly higher, indicating that P limitation increases during successional development. Due to the P limitation in this study area, P resorption efficiency and proficiency were higher than corresponding N resorption parameters. Dominant tree species at early‐successional stage adopted “conservative consumption” nutrient use strategy, whereas the species at late‐successional stage inclined to adopt “resource spending” strategy.
Kinetics of 125I‐PDGF binding and down‐regulation of PDGF receptor in human arterial smooth muscle cell strains during cellular senescence in vitro

Platelet‐derived growth factor (PDGF) is one of the major mitogens in serum to stimulate replication of human smooth muscle cells (SMCs) in culture. Previous studies using human fibroblasts failed to demonstrate changes in the receptor systems for growth factors during cellular senescence. We investigated the kinetics of 125I‐PDGF(‐BB) binding and down‐regulation of the PDGF receptor in three human arterial SMC strains during cellular aging. The number of specific 125I‐PDGF binding sites per cell increased slightly at a population doubling level (PDL) of 60%–80% of life span and then decreased at the PDL above 90%. The number of receptors per cell‐surface area decreased with increasing in vitro age. The apparent Kd for the 125I‐PDGF binding decreased with in vitro senescence. The internalization and degradation of 125I‐PDGF per receptor were significantly reduced in senescent SMCs than young cells. Furthermore, down‐regulation of the PDGF receptor was significantly greater in sensescent SMCs than young cells. Immunoblot studies demonstrated that changes in b̃‐subunit of the PDGF receptor accounted for those in the studies using 125I‐PDGF and that tyrosine phosphorylation of the PDGF receptor was significantly greater in young SMCs than aged cells. Our results suggest that age‐related changes in the receptor systems for PDGF may be important contributors to the failure of DNA synthesis in senescent SMCs. © 1995 Wiley‐Liss, Inc.
Revisiting the Role of Interleukin-1 Pathway in Osteoarthritis: Interleukin-1α and -1β, and NLRP3 Inflammasome Are Not Involved in the Pathological Features of the Murine Menisectomy Model of Osteoarthritis

Background: Innate immune response components such as toll-like receptors (TLRs) and NLRP3-inflammasome act in concert to increase IL-1α/β secretion by synovial macrophages. Previous results suggest that IL-1α/β could be an important mediator involved in the pathogenesis of osteoarthritis (OA). Objectives: The aim of our study was to evaluate the role of NLRP3, IL-1β, and IL-1α in the menisectomy (MNX) model of murine OA. Methods: Murine chondrocytes (CHs) and bone marrow-derived machrophages (BMDM) were stimulated with hydroxyapatite (HA) crystals, a form of calcium-containing crystal found in human OA, and IL-1β and IL-6 secretion assayed by ELISA.Conversely, the ability of IL-1β and IL-6 to induce CHs calcification was assessed in vitro by Alizarin red staining. Knees from 8 to 10 weeks old C57Bl/6J wild-type (WT) (n = 7), NLRP3−/− (n = 9), IL-1α−/− (n = 5), and IL-1β−/− (n = 5) mice were menisectomized, using the sham-operated contralateral knee as control. 8 weeks later, knee cartilage degradation and synovial inflammation were evaluated by histology. In addition, apoptotic chondrocytes, metalloproteases activity, and collagen-type 2 expression were evaluated in all mice. Joint calcification and subchondral bone parameters were quantified by CT-scan in WT and IL-1β−/− menisectomized knees. Results: In vitro, HA crystals induced significant increased IL-6 secretion by CHs, while IL-1β remained undetectable.Conversely, both IL-6 and IL-1β were able to increase chondrocytes mineralization. In vivo, operated knees exhibited OA features compared to sham-operated knees as evidenced by increased cartilage degradation and synovial inflammation. In menisectomized KO mice, severity and extent of cartilage lesions were similar (IL-1α−/− mice) or exacerbated (IL-1β−/− and NLRP3−/− mice) compared to that of menisectomized WT mice. Metalloproteases activity, collagen-type 2 expression, chondrocytes apoptosis, and synovial inflammation were similar between KO and WT mice menisectomized knees. Moreover, the extent of joint calcification in osteoarthritic knees was comparable between IL-1β−/− and WT mice. Conclusions: MNX knees recapitulated features of OA, i.e, cartilage destruction, synovial inflammation, cell death, and joint calcification. Deficiency of IL-1α did not impact on the severity of these features, whereas deficiency of IL-1β or of NLRP3 led to increased cartilage erosion. Our results suggest that IL-1α and IL-1β are not key mediators in this murine OA model and may explain the inefficiency of IL-1 targeted therapies in OA.
Rationale, design, and methods of the Preschool ADHD Treatment Study (PATS).

OBJECTIVE To describe the rationale and design of the Preschool ADHD Treatment Study (PATS). METHOD PATS was a National Institutes of Mental Health-funded, multicenter, randomized, efficacy trial designed to evaluate the short-term (5 weeks) efficacy and long-term (40 weeks) safety of methylphenidate (MPH) in preschoolers with attention-deficit/hyperactivity disorder (ADHD). Three hundred three subjects ages 3 to 5.5 years old who met criteria for a primary DSM-IV diagnosis of ADHD entered the trial. Subjects participated in an 8-phase, 70-week trial that included screening, parent training, baseline, open-label safety lead-in, double-blind crossover titration, double-blind parallel efficacy, open-label maintenance, and double-blind discontinuation. Medication response was assessed during the crossover titration phase using a combination of parent and teacher ratings. Special ethical considerations throughout the trial warranted a number of design changes. RESULTS This report describes the design of this trial, the rationale for reevaluation and modification of the design, and the methods used to conduct the trial. CONCLUSIONS The PATS adds to a limited literature and improves our understanding of the safety and efficacy of MPH in the treatment of preschoolers with ADHD, but changes in the design and problems in implementation of this study impose some specific limitations that need to be addressed in future studies.
Evidence for regional heterogeneity in corticotropin‐releasing factor interactions in the dorsal raphe nucleus

The dorsal raphe nucleus (DR) is innervated by fibers containing the stress‐related neurohormone corticotropin‐releasing factor (CRF), which alters DR neuronal activity and serotonin release in rats. This study examined the relative distribution of CRF‐immunoreactive fibers in the rat DR by using light level densitometry. Additionally, CRF‐immunoreactive processes within specific subregions of the DR were examined at the ultrastructural level by using electron microscopy. CRF‐immunoreactive fibers were organized within the DR along a caudal‐rostral gradient, such that proceeding rostrally, innervation shifted from dorsolateral to ventromedial. Numerous CRF‐immunoreactive axon terminals containing dense‐core vesicles were found in both the caudal dorsolateral region and the rostral ventromedial/interfascicular region. These formed synaptic specializations with unlabeled dendrites and frequently contacted nonlabeled axon terminals. Semiquantitative analysis revealed certain differences between the two regions with respect to the types of associations made by CRF‐immunoreactive terminals. Associations with dendrites were more frequent in the dorsolateral vs. ventromedial region (65% of 171 terminals vs. 39% of 233 terminals, respectively), whereas associations with axon terminals were more frequent in the ventromedial/interfascicular vs. the dorsolateral region (72% of 233 terminals vs. 57% of 171 terminals, respectively). Additionally, synaptic specializations between CRF‐immunoreactive terminals and dendrites were more frequently asymmetric in the dorsolateral region (60%) and symmetric (49%) in the ventromedial/interfascicular region. Regional differences in CRF terminal interactions in the DR could account for the reported heterogeneous effects of CRF on DR neuronal activity and forebrain serotonin release. Importantly, the present results provide anatomical substrates for regulation of the DR by endogenous CRF. J. Comp. Neurol. 435:450–463, 2001. © 2001 Wiley‐Liss, Inc.
Agile Methodologies in Software Maintenance: A Systematic Review

Agile Methodologies has been gaining popularity since 2000. The Software Maintenance phase of software lifecycle is the most expensive and tedious in nature and use of Agile methodologies helps in maintaining software over time in flexible and iterative manner. This study reviews several papers with different case studies to evaluate the performance and quality of software using agile methodologies. In this study, more than 30 research studies are investigated which are conducted between 2001 and 2015 and have been categorized according to the publication year, datasets, tools, type of techniques etc. This will be the first review paper on the use of the Agile in software maintenance which will help the researchers and encourages companies and beginners to adopt these methodologies to gain software quality. This study would also be helpful to professional academicians to identify the current trends and future gaps in the field of agile methodologies.
Understanding the Roles of Organizational Identification, Trust and Corporate Ethical Values in Employee Engagement–Organizational Citizenship Behaviour Relationship: A Study on Indian Managers

The rationale of the study is to comprehend the roles of organizational identification, trust and corporate ethical values (CEV) in employee engagement–organizational citizenship behaviour (OCB) relationship. The study was administered on 246 middle-level managers who were representatives of 30 different public and private sector organizations in Delhi National Capital Region. The results of the study confirmed the hypotheses. The results of the study confirmed that organizational identification, trust and CEV moderate the employee engagement–OCB relationship. Organizations need to recognize that OCB are helping behaviours contributing appreciably to organizational effectiveness; such behaviours daub the social machinery of the organizations, plummeting conflicts and thereby augmenting organizational effectiveness. These behaviours offer a litheness, which goes beyond the job description and provides direction to work behaviour of individuals in organization. Understanding the relationship between these variables will help both public and private sector organizations about the role of organizational identification, trust and CEV in employee engagement–OCB relationship.
The Potential Role of Endometrial Nerve Fibers in the Pathogenesis of Pain During Endometrial Biopsy at Office Hysteroscopy

We aimed to evaluate whether nerve fibers are present in the endometrial layer of patients submitted to office hysteroscopy and their potential contribution to the pathogenesis of pain during that procedure. Through a prospective case–control study performed in tertiary centers for women’s health, endometrium samples were collected during operative office hysteroscopy from 198 cycling women who previously underwent laparoscopy and/or magnetic resonance imaging investigation for infertility assessment. Samples were classified according to the degree of the pain patients experienced and scored from values ranging from 0 (absence of discomfort/pain) to 10 (intolerable pain) on a 10-cm visual analog scale (VAS). The presence of nerve fiber markers (S100, NSE, SP, VIP, NPY, NKA, NKB, NKR1, NKR2, and NKR3) in the endometrium was also evaluated by morphologic and immunohistochemical analyses. We found that S-100, NSE, NKR1, NK-A, NK-B, VIP, and NPY, were immunolocalized in samples of endometrium, in significantly (P < .01, for all) higher levels in samples collected from patients with VAS score > 5 (group A) than ≤ 5 (group B) and significantly (P < .0001 for all) positively correlated with VAS levels. A statistically significant (P = .018) higher prevalence of endometriosis and/or adenomyosis was depicted in patients of group A than group B. Data from the present study led us to conclude that nerve fibers are expressed at the level of the functional layer of the endometrium and may contribute to pain generation during office hysteroscopy, mainly in women affected by endometriosis and adenomyosis.