bluuebunny/crossref_metadata_2025 huggingface dataset:
51 CASPASE-3 INHIBITOR Z-VAD-FMK ENHANCES CRYOTOLERANCE OF IN VITRO-PRODUCED BOVINE PRE-IMPLANTATION EMBRYOS
Authors: Pero M. E. , Zullo G. , De Canditiis C. , Albero G. , Longobardi V. , Salzano A. , Varchetta R. , Gasparrini B.
Published: December 2016

In vitro-produced (IVP) bovine embryos are still less viable and resistant to cryopreservation than their in vivo counterparts. Cryopreservation induces cell degeneration through the apoptotic pathway in bovine oocytes and embryos (Men et al. 2003 Cryobiology 47, 73–81). Apoptosis can be prevented by inhibition of caspase activity, leading to improved cryosurvival in mammalian cells (Stroh et al. 2002 FASEB J. 16, 1651–3). Interestingly, cryotolerance of porcine embryos was improved by inhibiting apoptosis using a caspase inhibitor, benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone (Z-VAD-FMK) during vitrification and subsequent culture (Men et al. 2006 Theriogenology 66, 2008–16). Aim of this work was to evaluate whether cryotolerance of bovine IVP embryos may be improved by using Z-VAD-FMK during cryopreservation and post-warming in vitro culture. Abattoir-derived bovine oocytes (n = 753, over 4 replicates) were in vitro matured and fertilized according to standard procedures (Rubessa et al. 2011 Theriogenology 76, 1347–55). Twenty hours after IVF, presumptive zygotes were cultured in SOF medium at 39°C with 5% CO2, 7% O2, and 88% N2. On Day 7, embryo yields were assessed and blastocysts (except the hatched blastocysts) were randomly divided in 2 groups: vitrification and post-warming culture in presence (n = 60) or absence (n = 54) of 20 µM Z-VAD-FMK. Vitrification was carried out by Cryotop in 16.5% ethylene glycol, 16.5% DMSO, and 0.5 M sucrose (Rubessa et al. 2011 Theriogenology 76, 1347–55). Blastocysts were warmed in decreasing sucrose solutions (0.25 M for 1 min and 0.15 M for 5 min) and cultured for 2 days. Resistance to cryopreservation was evaluated by assessing the survival rate, based on morphological criteria and hatching rate after 48 h culture. Furthermore, TUNEL staining was used to evaluate the total cell (TC) number and the apoptotic rate of vitrified blastocysts after 48-h post-warming culture. Differences between groups in survival and hatching rates after 48-h post-warming culture were analysed by Chi-squared test, whereas differences in TC number and in number and percentage of apoptotic cells were analysed by Student’s t-test. Inhibition of caspase activity induced by Z-VAD-FMK increased embryo cryotolerance, as indicated by higher survival (92.6 v. 55.0%; P < 0.01) and hatching rates (40.7 v. 23.3%; P < 0.05) after 48 h of post-warming culture. Furthermore, Z-VAD-FMK decreased both the average number (7.1 ± 0.6 v. 4.2 ± 0.3; P < 0.01) and the percentage (6.3 ± 0.6 v. 3.0 ± 0.2; P < 0.01) of apoptotic cells in blastocysts. No differences were recorded in TC number between groups (on average, 128.90 ± 1.6). These results suggest that addition of 20 µM Z-VAD-FMK during vitrification/warming and post-warming culture significantly inhibits apoptosis (DNA fragmentation) and improves the cryotolerance of IVP bovine embryos.
62 BOVINE OCT4 (POU5F1) KNOCKOUT EMBRYOS FAIL DURING THE SECOND LINEAGE DIFFERENTIATION DUE TO LOSS OF NANOG
Authors: Simmet K. , Klymiuk N. , Zakhartchenko V. , Güngör T. , Reichenbach M. , Reichenbach H.-D. , Wolf E.
Published: December 2016

We generated a CRISPR/Cas9 mediated knockout (KO) of the OCT4 gene in adult fibroblasts, where biallelic deletion of a single nucleotide leads to a frameshift mutation. Through reconstruction of embryos by somatic cell NT, we were able to study the role of OCT4 during pre-implantation development until Day 7 in vitro. The presence of OCT4 protein was evaluated after immunofluorescent staining by confocal laser scanning microscopy of Day 5 morulae and Day 7 blastocysts; somatic cell NT embryos reconstructed from nontransfected cells of the same source served as control. Whereas control morulae expressed OCT4 in all cells, OCT4 KO morulae showed expression in only 67.8 ± 11.1% (mean ± SD, n = 6) of cells and overall intensity was decreased. By Day 7, no expression of OCT4 was detected in OCT4 KO blastocysts (n = 24), suggesting that maternal stores of the OCT4 protein had decayed. In contrast, control blastocysts (n = 20) showed OCT4 expression ubiquitously in both inner cell mass (ICM) and trophectoderm (TE). Simultaneously to the OCT4 staining, we differentially stained ICM and TE with the TE specific marker CDX2 and counterstained cell nuclei with 4′,6-diamidino-2-phenylindole. No significant differences between OCT4 KO Day 7 blastocysts and controls were detected in total cell numbers (89.6 ± 27.5 v. 96.3 ± 38) and percentage of CDX2 positive cells (50.7 ± 16.8% v. 59.0 ± 20.8%) (P > 0.05, mean ± SD, unpaired, two-tailed t-test). To analyse the role of OCT4 during the second lineage differentiation, we stained Day 5 morulae and Day 7 blastocysts for the epiblast and hypoblast specific markers NANOG and GATA6, respectively. In morulae, both markers were present and co-expressed in OCT4 KO and control embryos. By Day 7, control blastocysts (n = 6) already showed the typical salt and pepper distribution of NANOG and GATA6 positive cells, but expression was not mutually exclusive in all cells and also not restricted to ICM. OCT4 KO embryos lost all NANOG expression at Day 7 blastocyst stage (n = 8) and only stained positive for GATA6 in both TE and ICM. We conclude that OCT4 is not required for the quantitative allocation of cells to either the ICM or the TE during the first lineage differentiation, as total cell number and percentage of CDX2 positive cells was unchanged. Additionally, expression of NANOG seems to be OCT4 dependent and OCT4 KO embryos fail to establish the epiblast lineage—unlike mouse Oct4 KO embryos, where developmental failure was connected to loss of GATA6 expression during second lineage differentiation.
This work was funded by the Bavarian Research Foundation (AZ-1031–12).
97 PRELIMINARY DESCRIPTIVE STUDY OF EQUINE PLACENTA GENERATED AFTER TRANSFER OF IN VIVO- AND IN VITRO-PRODUCED EMBRYOS
Authors: Lanci A. , Mariella J. , Merlo B. , Castagnetti C. , Iacono E.
Published: December 2016

Placental changes associated with artificial reproductive technologies have been described in several species, but little information is available in horses. Joy et al. (2012) reported that human placentas from intracytoplasmic sperm injection derived embryos were heavier and thicker than those produced after natural conception. Despite the most growing interest and efficiency of artificial reproductive technologies in equine species, only recently, Pozor et al. (2016) described placental abnormalities in pregnancies generated by somatic cell NT, but there are no studies on equine placenta generated by intracytoplasmic sperm injection and traditional embryo transfer. In the present preliminary study, macroscopic differences of placentas generated after transfer of in vitro- or in vivo-produced embryos were registered. Twelve Standardbred recipient mares with pregnancy generated after transfer of in vivo-derived (Group 1) and in vitro-derived (Group 2) embryos were enrolled; 10 Standardbred mares with pregnancy derived by traditional AI were included as control (Group 3). All pregnancies were physiological, and newborn foals were healthy. Mare age, parity, length of pregnancy, gross evaluation and weight of placenta, total length of umbilical cord (UC), length of UC, number of UC coils, foal sex, and weight at birth were registered. Collected data are listed in Table 1 and are expressed as mean ± standard deviation. Differences between groups were evaluated by 1-way ANOVA, and the difference in proportion of overweight placentas was evaluated with the Fisher test. The gross evaluation of placenta revealed 8/12 placentas (2/4 Group 1; 6/8 Group 2) were heavier than 11% (Madigan, 1997) due to oedema of the chorioallantois. No overweight placentas were registered in Group 3. In Group 1, 1/4 placentas had villous hypoplasia, and in Group 2, 1/8 placentas had cystic pouches on the UC. There were no significant differences among groups. However, the proportion of overweight placentas between Group 2 (6/8) and Group 3 (0/10) approached significance (P = 0.06). Although preliminary, the results of the present study suggest that production of equine embryos in vitro may lead to alterations in placental development. Several studies in cattle and sheep have suggested that alterations in the placentas of pregnancies derived from in vitro-produced embryos are related to effects of culture on epigenetic regulation. Less is known in the horse about the effects of in vitro embryo production on placental development; thus, further research in this area is necessary.

Table 1.

Characteristics of full-term placentas derived from AI or embryo transfer with in vivo- and in vitro-produced embryos
99 BIRTH OF THE FIRST BOVINE EMBRYO TRANSFER CALF IN THE REPUBLIC OF KOSOVA
Authors: Behluli B. , Jahnke M. , West J. K. , Youngs C. R.
Published: December 2016

The objective of this applied field study was to assess the feasibility of successfully performing bovine embryo transfer in the Republic of Kosova—a feat that had not yet been accomplished in this newly independent (2008) eastern European country. Three Holstein heifers at the Iowa State University dairy farm were superovulated with a conventional descending dose regimen of FSH (Folltropin). Approximately 12 and 24 h after the observed onset of oestrus, heifers were inseminated with semen from a single Red Holstein bull. Embryos were non-surgically collected and washed in accordance with IETS procedures for sanitary handling of embryos. Embryos were cryopreserved for subsequent direct transfer. After obtaining an import permit from the Kosovo Food and Veterinary Agency, embryos were approved for export to the Republic of Kosova by the US Department of Agriculture, Animal Plant Health Inspection Service. Embryos were shipped via an express courier service. A total of 19 embryos were received in the Republic of Kosova. Recipients were monitored for signs of naturally occurring oestrus, and immediately before transfer, embryos were thawed by holding in air for 3 to 5 s followed by placement into a 37°C water bath for 25 to 30 s. The first-ever bovine embryo transfer calf in the Republic of Kosova was born July 6, 2015. A total of 9 calves were born from the 19 embryos transferred (47.4% embryo survival rate). Results of this applied field study show that bovine embryo transfer is feasible in the Republic of Kosova. Embryo transfer will be used to improve the quality of dairy cattle genetics in the Republic of Kosova and to subsequently increase the national supply of milk, decrease dependence on milk imports, and increase food security of the nation.
Working memory, language processing, and implications of malleability for second language acquisition
Authors: Tsai Nancy , Au Jacky , Jaeggi Susanne M.
Published: December 2016

Working memory is thought of as a fundamental cognitive system that is particularly important for complex cognition such as language processing. Individuals differ in the amount of information they can keep in working memory, and such differences predict language processing and acquisition, including second language (L2) learning. Given its relevance for higher order cognition, interventions targeting WM have proliferated in recent years, on the premise that improving WM skills might also improve other cognitive functions relying on WM. Accumulating evidence is promising in that certain interventions do result in language-related improvements that go beyond task-specific practice. Given the importance of WM in L2 acquisition, we propose that WM interventions might be a promising avenue to facilitate L2 learning.
Music, song and speech
Authors: Christiner Markus , Reiterer Susanne
Published: December 2016

Recent evidence shows that musical aptitude positively influences language acquisition processes. The underlying mechanisms of why and how musical talent heightens one’s ability to detect, imitate and memorize foreign languages, however, have not yet been fully understood. We set out to test vocalists’ ability to imitate speech. Findings indicated that singing capacity is a good predictor for accent imitation and a better predictor of than instrument playing and musical expertise measured perceptually. As we wanted to uncover whether there is a difference between instrumentalists’ and vocalists’ accent imitation abilities, we recruited vocalists, instrumentalists and non-singers/non-musicians and compared their accent imitation skills directly. As expected, vocalists outperformed instrumentalists and non-musicians/non-singers significantly, while the perceptual musicality test showed no significant difference between vocalists and instrumentalists.
Elicited imitation as a measure of implicit L2 knowledge
Authors: Granena Gisela
Published: December 2016

Elicited imitation (EI) is an oral production task considered to be conducive to the retrieval of implicit second language (L2) knowledge (e.g. Bley-Vroman & Chaudron 1994; Chaudron, Prior, & Kozok 2005; Ellis 2005; Erlam 2006). This study aimed at contributing to testing the validity of EI as a measure of implicit language knowledge by examining whether individual differences in working memory (WM) and/or short-term memory (STM) capacity are related to performance on an EI task. The study focused on two types of morpho-syntactic agreement: plural marking and third person subject-verb agreement in English. Sixty intermediate-level learners of English with Chinese as L1 background participated in the study. The results of the study showed that neither WM nor STM moderated accuracy scores on the EI task. These findings were interpreted as evidence of automatic knowledge retrieval during the task and, therefore, as evidence in support of the validity of EI as a measure of implicit language knowledge.
Executive control and phonological processing in language acquisition
Authors: Darcy Isabelle , Mora Joan C.
Published: December 2016

This chapter discusses the relationship between cognitive control and phonological processing in a second language (L2). Cognitive control is globally referred to as executive functions, mainly consisting of attention control, working memory and inhibitory control. Our research examines how dealing with multiple languages early on relates to differences in cognitive abilities, and how individual differences in cognitive abilities in turn impact phonological processing in L2. Building on evidence that functional bilinguals develop fine-grained advantages in cognitive control over monolinguals (Bialystok 2011), we investigate whether language learners with greater cognitive control are also better equipped to acquire a new phonological system. We report on data from two groups of L2 learners (L1 Spanish) who started learning English during adolescence. One group of learners grew up in a Spanish monolingual environment; the other grew up in a bilingual environment (Spanish/Catalan). The early bilingual participants used both Catalan and Spanish daily, but differed in the amount of use of their less dominant language (either Catalan or Spanish). We measured attention control, phonological memory and inhibitory control, and assessed L2 phonological processing skills via a perception task. The results indicate that phonological short-term memory and inhibition are related to L2-phonological processing, but not in the same way for all groups. The relationship interacts with the participants’ linguistic profile. Specifically, inhibitory control strongly correlates with L2 phonological processing for the participants from the monolingual environment: participants with stronger inhibitory control were more accurate in the perception task. This relationship was not visible for the participants with bilingual experience. We propose that the effects of individual differences in inhibitory control for these bilinguals might have been “washed out” due to the daily practice they receive in inhibiting one language over the other.
The role of explicit language aptitude in implicit, explicit, and mixed feedback conditions
Authors: Yilmaz Yucel , Granena Gisela , Meyer Zachary S.
Published: December 2016

This study examined whether there is any relationship between second language (L2) learning outcomes under different negative feedback conditions and cognitive abilities for language learning that involve explicit cognitive processes (i.e. explicit language aptitude). The study followed a pretest, immediate posttest, delayed posttest design, and used a set of controlled oral production tests as outcome measures. Between the pretest and the immediate posttest, 80 L2 learners of English carried out three oral production tasks, in which their errors on the indefinite article were treated according to the group they had been assigned to (i.e. explicit, implicit, mixed, reduced explicit or no-feedback). Three subtests from the LLAMA Language Aptitude Test battery (Meara 2005) were used to test the learners’ explicit language aptitude. Results showed that only on the immediate posttest and only under the explicit feedback condition was explicit language aptitude predictive of L2 performance.
Star formation law in the Milky Way
Authors: Sofue Yoshiaki , Nakanishi Hiroyuki
Published: December 2016

The Schmidt law (SF law) in the Milky Way was investigated using 3D distribution maps of H ii regions and H i and molecular (H2) gases with spatial resolutions of ∼1 kpc in the Galactic plane and a few tens of pc in the vertical direction. H ii regions were shown to be distributed in a star-forming (SF) disk with nearly constant vertical full thickness 92 pc in spatial coincidence with the molecular gas disk. The vertically averaged volume star formation rate (SFR) ρSFR in the SF disk is related to the surface SFR ΣSFR by ρSFR/[M⊙ yr−1 kpc−3] = 9.26 × ΣSFR/[M⊙ yr−1 kpc−2]. The SF law fitted by a single power law of gas density in the form of $\Sigma _{\rm SFR}\propto \rho _{\rm SFR}\propto \rho _{\rm gas}^\alpha$ and $\propto \Sigma _{\rm gas}^\beta$ showed indices of α =0.78 ± 0.05 for $\rho _{\rm H_2}$ and 2.15 ± 0.08 for ρtotal, and β = 1.14 ± 0.23 for Σtotal, where ρ and Σ denote volume and surface densities, respectively. The star formation rate is shown to be directly related to the molecular gas, but indirectly to H i and total gas densities. The dependence of the SF law on the gaseous phase is explained by the phase transition theory between H i and H2.
Metformin-Induced Generalized Fixed Drug Eruption With Cutaneous Hemophagocytosis
Authors: Ramírez-Bellver Jose Luis , Lopez Joaquin , Macias Elena , Fuertes Laura , Andres Irene , Alegria Victoria , Gimeno Ignacio , Perez Alejandra , Perez Yosmar , Requena Luis
Published: December 2016

Fixed drug eruption (FDE) consists of recurrent dusky-red to brownish macules or patches at the same sites after the readministration of the causative drug. It usually presents as a solitary lesion, but generalized eruptions have been described. The most frequently implied drugs are antibiotics, anticonvulsants, and analgesics. Only 2 cases due to metformin have been reported. Histopathologic features of FDE include vacuolar degeneration of the basal layer, necrotic keratinocytes, and superficial and deep perivascular lymphocytic infiltrate. Cutaneous hemophagocytosis in the context of a FDE has not been previously reported. We describe the case of an 86-year-old man who developed a pruritic generalized macular eruption of reddish to violaceous patches. Skin biopsy was performed and the dermal infiltrate was immunohistochemically studied. Histopathology showed interface dermatitis with vacuolar degeneration of the basal layer, necrotic keratinocytes, and superficial and deep perivascular lymphohistiocytic infiltrate. In deep dermis, histiocytes with engulfed cells inside their cytoplasm were seen. Lymphoid enhancer binding factor 1 immunostain demonstrated that most of these cells were lymphocytes. We present the first case with cutaneous hemophagocytosis in the context of a metformin-induced generalized FDE. In this particular case, hemophagocytosis was just a histopathologic finding with no systemic consequences for the patient.
Systemic Contact Dermatitis and Low-Allergen Diets
Authors: Weiss Emma , Katta Rajani
Published: December 2016

Systemic contact dermatitis is a skin reaction that occurs after systemic exposure to a previously encountered allergen. Such exposure may occur via oral, intravenous, percutaneous, or inhalational routes. After exposure, dermatitis may occur at various sites. One clue to the diagnosis is the occurrence of recurrent episodes of contact dermatitis despite topical avoidance of known allergens. The treatment of systemic contact dermatitis involves avoidance of all systemic exposure to an allergen, which includes removal of the allergen from the diet. In this review, we focus on four major dietary allergens and describe relevant dietary sources to serve as a guide for patient education. These allergens are nickel, balsam of Peru, propylene glycol, and formaldehyde.
Awareness of Cervical Cancer Causes and Predeterminants of Likelihood to Screen Among Women in Haiti
Authors: McCarthy Schatzi H. , Walmer Kathy A. , Boggan Joel C. , Gichane Margaret W. , Calo William A. , Beauvais Harry A. , Brewer Noel T.
Published: December 2016

Objectives

Cervical cancer is the leading cause of cancer deaths among women in Haiti. Given this high disease burden, we sought to better understand women's knowledge of its causes and the sociodemographic and health correlates of cervical cancer screening.

Materials and Methods

Participants were 410 adult women presenting at clinics in Léogâne and Port-au-Prince, Haiti. We used bivariate and multivariate logic regression to identify correlates of Pap smear receipt.

Results

Only 29% of respondents had heard of human papillomavirus (HPV), whereas 98% were aware of cervical cancer. Of those aware of cervical cancer, 12% believed that sexually transmitted infections (STIs) cause it, and only 4% identified HPV infection as the cause. Women with a previous sexually transmitted infection were more likely to have had Pap smear (34% vs 71%, odds ratio = 3.45; 95% CI = 1.57–7.59). Screening was also more likely among women who were older than the age of 39 years, better educated, and employed (all p < .05). Almost all women (97%) were willing to undergo cervical cancer screening.

Conclusions

This sample of Haitian women had limited awareness of HPV and cervical cancer causes; but when provided with health information, they saw the benefits of cancer screening. Future initiatives should provide health education messages, with efforts targeting young and at-risk women.
Polycystic ovary syndrome in adolescent girls
Authors: Baldauff Natalie Hecht , Witchel Selma Feldman
Published: December 2016

Purpose of review

Polycystic ovary syndrome (PCOS) is a common heterogeneous disorder that appears to have its origins during the peripubertal years. The diagnostic conundrum is that the typical clinical features, irregular menses and acne, occur during normal female puberty. Understanding the physiologic origins and molecular basis of the dysregulated hypothalamic–pituitary–gonadal axis in PCOS is fundamental to interrupting the distinctive vicious cycle of hyperandrogenism and chronic anovulation.

Recent findings

Newer ultrasound technology with better spatial resolution has generated controversy regarding the optimal imaging criteria to define polycystic ovary morphology. Using such equipment, the Androgen Excess PCOS Society Task Force Report recommends a threshold of at least 25 follicles per ovary as the definition of polycystic ovary morphology. The implementation and results of genome-wide association studies has opened a new window into the pathogenesis of PCOS. Recent genome-wide association studies have identified several loci near genes involved in gonadotropin secretion, ovarian function, and metabolism. Despite the impediments posed by phenotypic and genetic heterogeneity among women with PCOS, investigation into one locus, the DENND1A gene, is providing insight into the ovarian steroidogenesis. Anti-Mullerian hormone (AMH) has long been recognized to play a major role in the ovarian dysfunction. Recent animal data implicate AMH in the neuroendocrine dysregulation by demonstrating AMH-stimulated increased gonadotropin releasing hormone and luteinizing hormone secretion.

PCOS is a common complex multifaceted disorder associated with genetic and environmental influences affecting steroidogenesis, steroid metabolism, neuroendocrine function, insulin sensitivity, pancreatic β cell function, and alternative adaptations to energy excess. Current research into the genetics and pathophysiology is reviewed. The difficulties inherent in diagnosing PCOS in adolescent girls are discussed.
Routine Inpatient Human Immunodeficiency Virus Screening
Authors: Baker Daniel C.
Published: December 2016

Purpose/Objectives:

This article reviews the current guidelines for human immunodeficiency virus (HIV) screening among inpatients and explores adherence to the guidelines and barriers to their implementation.

Background:

In 2006, the Centers for Disease Control and Prevention released updated recommendations suggesting HIV screening for all patients in all healthcare settings.

Description:

A nonsystematic review of current HIV screening guidelines, as well as research and nonresearch literature, addressing rates of inpatient screening was performed.

Results:

Between 2000 and 2010, there was a significant increase in testing in healthcare settings. Despite these advances, 10 years after the updated Centers for Disease Control and Prevention guidelines were released, many hospitals still have not fully implemented the recommendations. Barriers to implementation of the guidelines include provider misconceptions and lack of time and reimbursement.

Conclusions:

Screening for HIV identifies new infections, reduces transmission, prevents complications, and encourages a discussion about prevention. Increasing adherence to screening recommendations can help prevent new cases and disease progression. The nursing focus on prevention makes clinical nurse specialists and other advanced practice registered nurses uniquely positioned to increase screening. Clinical nurse specialists should implement research projects to understand adherence in their facilities and identify and address site-specific barriers. Quality improvement programs can then be implemented to improve screening rates.
A comparative microarray analysis identifies a conserved gene expression signature between airway injury and lung cancer
Authors: Giangreco Adam
Published: December 2016

Lung squamous cell carcinoma (SqCC) accounts for 30% of lung cancers, with over 400,000 deaths per year worldwide. Although evidence suggests that chronic lung injury drives carcinogenesis, a comprehensive understanding of this process remains elusive. Here, I used a comparative microarray analysis to identify gene expression differences shared between airway injury and squamous lung cancer. Of the 667 genes that exhibited differential expression following murine polidocanol and SO2 injury, 40.6% were additionally dysregulated in human SqCC. Among these, 150 genes were consistently upregulated and 54 downregulated relative to all controls. Examples included genes associated with increased cell cycling, aberrant cytokinesis and DNA repair, and enhanced tumour cell invasion and metastases. For 88.2% of identified genes, altered expression was associated with increased SqCC progression and patient mortality. These results establish a novel gene expression signature linking airway injury and lung cancer pathogenesis.
Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-Seq data
Authors: Teng Mingxiang , Irizarry Rafael A.
Published: December 2016

The main application of ChIP-seq technology is the detection of genomic regions that bind to a protein of interest. A large part of functional genomics public catalogs are based on ChIP-seq data. These catalogs rely on peak calling algorithms that infer protein-binding sites by detecting genomic regions associated with more mapped reads (coverage) than expected by chance as a result of the experimental protocol's lack of perfect specificity. We find that GC-content bias accounts for substantial variability in the observed coverage for ChIP-Seq experiments and that this variability leads to false-positive peak calls. More concerning is that GC-effect varies across experiments, with the effect strong enough to result in a substantial number of peaks called differently when different laboratories perform experiments on the same cell-line. However, accounting for GC-content in ChIP-Seq is challenging because the binding sites of interest tend to be more common in high GC-content regions, which confounds real biological signal with the unwanted variability. To account for this challenge we introduce a statistical approach that accounts for GC-effects on both non-specific noise and signal induced by the binding site. The method can be used to account for this bias in binding quantification as well to improve existing peak calling algorithms. We use this approach to show a reduction in false positive peaks as well as improved consistency across laboratories.
Colony Lift Colorimetric Assay for β-Galactosidase Activity
Authors: Fuxman Bass Juan I. , Reece-Hoyes John S. , Walhout Albertha J.M.
Published: December 2016

In this protocol, we present a qualitative assay for monitoring the level of expression of β-galactosidase, an enzyme encoded by the LacZ gene, in yeast. This is useful both for determining autoactivity of LacZ expression in yeast DNA “bait” strains and for assessing LacZ reporter gene activation mediated by a transcription factor “prey” interaction with a DNA bait of interest in yeast one-hybrid (Y1H) assays. In this colorimetric assay, yeast are lysed in liquid nitrogen and then assayed for β-galactosidase expression using the colorless compound X-gal, which turns blue in the presence of this enzyme.
Zymolyase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast
Authors: Fuxman Bass Juan I. , Reece-Hoyes John S. , Walhout Albertha J.M.
Published: December 2016

Here, we present a protocol for amplifying DNA fragments from the genome of, or plasmids transformed into, yeast strains that require the use of the lytic enzyme zymolyase to break open the yeast cells by digesting the cell wall. Yeast strains requiring such treatment include YM4271 and Y1HaS2, whereas other yeast strains (e.g., MaV103) might not require treatment with Zymolyase.
Measurement of Metabolome Samples Using Liquid Chromatography–Mass Spectrometry, Data Acquisition, and Processing
Authors: Pluskal Tomáš , Yanagida Mitsuhiro
Published: December 2016

We present a protocol for metabolomic sample measurement using hydrophilic interaction chromatography (HILIC) combined with high-resolution Orbitrap mass spectrometry (MS). We also introduce a raw data processing method using MZmine 2 software, and include a list of 111 metabolite peaks (with their m/z values and retention times) previously identified in metabolome samples using this method.
In the Midst of Life—Cell Death: What Is It, What Is It Good for, and How to Study It
Authors: Silke John , Johnstone Ricky W.
Published: December 2016

Cell death, one of the most fundamental biological processes, has not made it into the public consciousness in the same way that genetic inheritance, cell division, or DNA replication has. Everyone knows they get their genes from their parents, but few would be aware that even before they were born a lot of essential cell death has shaped their development. The greater population, for the most part, is blissfully unaware that every day millions of their own cells die in a programmed way and that this is essential for normal human physiology—their well-being, in fact. Nowhere is the burial liturgy, “In the midst of life we are in death,” more apt. Despite this public underappreciation, cell death research is a major industry. A search in PubMed for “apoptosis,” a special form of cell death that is caused by caspases, returns approximately 280,000 hits. The intense research interest arises from the realization that abnormal cell death responses play an important role in two of the biggest killers in the western world: cancer and cardio/cerebrovascular disease. Furthermore, the manner in which cells die can also influence the development of autoimmune and autoinflammatory diseases. It is therefore of paramount importance to ensure that experiments accurately quantitate and correctly identify cell death in all its guises. That is the goal of this protocol collection.
Metabolomic Analysis of Schizosaccharomyces pombe: Sample Preparation, Detection, and Data Interpretation
Authors: Pluskal Tomáš , Yanagida Mitsuhiro
Published: December 2016

Metabolomics is a modern field of chemical biology that strives to simultaneously quantify hundreds of cellular metabolites. Techniques for metabolomic analysis in Schizosaccharomyces pombe have only recently been developed. Here we introduce methods that provide a complete workflow for metabolomic analysis in S. pombe. Based on available literature, we estimate the yeast metabolome to comprise on the order of several thousand different metabolites. We discuss the feasibility of extraction and detection of such a large number of metabolites, and the influences of various parameters on the results. Among the parameters addressed are cell cultivation conditions, metabolite extraction techniques, and detection and quantification methods. Further, we provide recommendations on data management and data processing for metabolomic experiments, and describe possible pitfalls regarding the interpretation of metabolomic data. Finally, we briefly discuss potential future developments of this technique.
Clustering of online learning resources via minimum spanning tree
Authors: Wu Qingyuan , Zhan Changchen , Wang Fu Lee , Wang Siyang , Tang Zeping
Published: December 2016

Purpose

The quick growth of web-based and mobile e-learning applications such as massive open online courses have created a large volume of online learning resources. Confronting such a large amount of learning data, it is important to develop effective clustering approaches for user group modeling and intelligent tutoring. The paper aims to discuss these issues.

Design/methodology/approach

In this paper, a minimum spanning tree based approach is proposed for clustering of online learning resources. The novel clustering approach has two main stages, namely, elimination stage and construction stage. During the elimination stage, the Euclidean distance is adopted as a metrics formula to measure density of learning resources. Resources with quite low densities are identified as outliers and therefore removed. During the construction stage, a minimum spanning tree is built by initializing the centroids according to the degree of freedom of the resources. Online learning resources are subsequently partitioned into clusters by exploiting the structure of minimum spanning tree.

Findings

Conventional clustering algorithms have a number of shortcomings such that they cannot handle online learning resources effectively. On the one hand, extant partitional clustering methods use a randomly assigned centroid for each cluster, which usually cause the problem of ineffective clustering results. On the other hand, classical density-based clustering methods are very computationally expensive and time-consuming. Experimental results indicate that the algorithm proposed outperforms the traditional clustering algorithms for online learning resources.

Originality/value

The effectiveness of the proposed algorithms has been validated by using several data sets. Moreover, the proposed clustering algorithm has great potential in e-learning applications. It has been demonstrated how the novel technique can be integrated in various e-learning systems. For example, the clustering technique can classify learners into groups so that homogeneous grouping can improve the effectiveness of learning. Moreover, clustering of online learning resources is valuable to decision making in terms of tutorial strategies and instructional design for intelligent tutoring. Lastly, a number of directions for future research have been identified in the study.
Leader legitimacy – a matter of education?
Authors: Lund Anne Kamilla
Published: December 2016

Purpose

The purpose of this paper is to discuss and share some practical insights on how leaders can seek legitimacy when leading highly specialized/highly educated people from other educational backgrounds than their own.

Design/methodology/approach

Based on an initial literature review on leader legitimacy, this paper distills three strategies for strengthening leader legitimacy that can apply to leaders of organizations employing highly specialized/highly educated people.

Findings

If these strategies are applied, leaders leading people from other educational backgrounds than their own will strengthen their possibilities for being perceived legitimate leaders. Further, for recruiters of leaders, awareness about the legitimacy challenge is an important step in choosing the “right” person for the job. For educational institutions and organizers of organizational-internal leader development programs, the strategies are important to consider when preparing and planning teaching on leadership.

Research limitations/implications

Research was based on a systematic literature review on leader legitimacy and the findings result from an initial categorizing.

Practical implications

The paper provides strategic insights and practical approaches with the potential to enhance leader and business effectiveness and informing leader-education approaches. The paper bridges theory and practice for leaders, recruiters of leaders and leader-education institutions.

Originality/value

The briefing saves busy executives and researchers hours of reading time by presenting pertinent information in a condensed and practice-oriented format.
The Kansas story: a sea of Koha green on the plains
Authors: Hastings Robin , Braum Heather , Willems Harry , Hutchinson Crystal , Santy Gail , Shafer Maribeth , Robb Jason , Carswell Roger
Published: December 2016

Purpose

Three of the seven regional systems in Kansas report on the history and use of the open-source Koha integrated library system (ILS) in their regions.

Design/methodology/approach

Each of the systems wrote up their experiences and then they collaborated on sections that discussed how they work together to achieve success with this product.

Findings

Each of the systems will continue to use the Koha software, and there are a few stand-alone instances of Koha already in place in Kansas. Development and advocacy of the product will be continued by all three of the systems.

Originality/value

This is a rare instance of three separate consortia coming together to work on improving everyone’s experience with an open-source ILS. The authors feel that the experiences they have had with this software are of value to anyone considering making use of it.
The true cost
Authors: Fox Robert
Published: December 2016

Purpose

This column takes a critical look at how technology projects are valued according to various cost factors. Those factors are examined, and a proposal is made regarding the use of agile scrum to overcome the limitations of standard cost analysis. Standard cost analysis based on time and financial burden limit the ability of library leadership to make innovative and visionary decisions concerning library strategy vis-à-vis technology.

Design/methodology/approach

This is a regular column. The material was written based on experience and familiarity with current issues as well as a literature review.

Findings

As this is a regular column that is exploratory and speculative in nature, there are no formal findings. The conclusion is based on the ideas presented in the column narrative.

Originality/value

The average approach to cost analysis, otherwise known as the return on investment, stifles the ability of library leadership to make strategic decisions that are focused on opportunities and relevance. Agile scrum is not simply a method to organize and manage software development projects. It transforms the thinking of an organization and establishes a decision-making model that places concerns at the appropriate level so that libraries can be nimble with regard to technology implementation.
Assessment of risk premium in farm technology adoption as a climate change adaptation strategy in the dryland systems of India
Authors: Kakumanu Krishna Reddy , Kuppanan Palanisami , Ranganathan C.R. , Shalander Kumar , Amare Haileslassie
Published: December 2016

Purpose

Changing climate has increasingly become a challenge for smallholder farmers. Identification of technical, institutional and policy interventions as coping and adaptation strategies and exploring risks of their adoption for smallholder farms are the important areas to consider. The aim of the present study was to carry out an in-depth analysis of adaptation strategies followed and the associated risk premium in technology adoption.

Design/methodology/approach

The study was carried out in the dryland systems of three Indian states – Andhra Pradesh, Karnataka and Rajasthan – and was based on a survey of 1,019 households in 2013. The flexible moment-based approach was used for estimating the stochastic production function, which allowed estimation of the relative risk premium that farmers are willing to pay while adopting the technologies to avoid crop production risks.

Findings

In all the three states, the risk premium (INR ha−1) was higher for farm mechanization compared to supplemental irrigation, except in the case of Andhra Pradesh. The higher the level of technology adoption, the higher the risk premium that households have to pay. This can be estimated by the higher investment needed to build infrastructure for farm mechanization and supplemental irrigation in the regions. The key determinants of technology adoption in the context of smallholder farmers were climatic shocks, investment in farm infrastructure, location of the farm, farm size, household health status, level of education, married years, expected profit and livestock ownership.

Originality/value

Quantification of the risk premium in technology adoption and conducting associated awareness programs for farmers and decision-makers are important to strengthen evidence-based adoption decisions in the dryland systems of India.
Developing a joint outcomes contracting model for integrated health and social care for older people
Authors: Billings Jenny , Davis Alison
Published: December 2016

Purpose

Current debates surrounding the NHS contract in England are suggesting that it is in need of change to support an integrated health and social care transformation agenda that meets the needs of an ageing chronically ill population. The purpose of this paper is to describe a three-phase project in England that sought to develop and validate a whole systems contracting model for integrated health and social care focusing on older people with long-term conditions, and based on joint outcomes.

Design/methodology/approach

A participative mixed-method approach for the development of the contracting model was used; this consisted of a literature review, a design phase drawing on consensus method through stakeholder discussions and an international validation phase.

Findings

The final contracting model consists of four overarching and interrelated core elements: outcomes; partnership, collaboration and leadership; financial: incentives and risk; and legal criteria. Each core element has a series of more detailed contracting criteria, followed by further specifications attached to each criteria.

Research limitations/implications

While the policy environment appears to be conducive to change and encourages the adoption of new ways of thinking, there are difficulties with the implementation of new innovative models that challenge the status quo, and this is discussed.

Practical implications

The paper concludes with reflections on the way forward for local development and implementation.

Originality/value

There is currently much discussion for the need to realign contracting for integrated care that has a better fit for the transformation agenda, but until now, there have been no attempts to develop a whole systems approach that focusses on joint outcomes. This research bridges the gap but recognizes the challenges to implementation.
OD, change management, and the a priori: introducing parrhesia
Authors: Sementelli Arthur Jay
Published: December 2016

Purpose

The purpose of this paper is to introduce a Foucauldian concept into the theory and practice of OD and change management. The piece challenges Habermasian a priori assumptions about organizational diagnosis and intervention.

Design/methodology/approach

This is a conceptual paper.

Findings

Literature points to the benefit of considering the possibility of parrhesiastic behavior in change management and organization development as part of a broader set of diagnostic tools.

Research limitations/implications

Future research should engage in practice driven test cases, interview practicing change managers, and refine the concept for use as a diagnostic tool.

Practical implications

Including discussions of parrhesia in change management and OD study and practices can better prepare change professionals for the realities of contemporary organizational practices.

Originality/value

To date, the links developed in this manuscript have not been made in the management literature, though it builds upon emerging literature in critical management studies and human resource management. It has the potential to influence both theory and practices of both OD and change management.
Recent trends in microwave assisted synthesis of fluorescent dyes
Authors: Elgemeie Galal H. , Masoud Doaa M.
Published: December 2016

Purpose

This paper aims to focus on the most popular technique nowadays, the use of microwave irradiation in organic synthesis; in a few years, most chemists will use microwave energy to heat chemical reactions on a laboratory scale. Also, many scientists use microwave technology in the industry. They have turned to microwave synthesis as a frontline methodology for their projects. Microwave and microwave-assisted organic synthesis (MAOS) has emerged as a new “lead” in organic synthesis.

Design/methodology/approach

Using microwave radiation for synthesis and design of fluorescent dyes is of great interest, as it decreases the time required for synthesis and the synthesized dyes can be applied to industrial scale.

Findings

The technique offers many advantages, as it is simple, clean, fast, efficient and economical for the synthesis of a large number of organic compounds. These advantages encourage many chemists to switch from the traditional heating method to microwave-assisted chemistry.

Practical implications

This review highlights applications of microwave chemistry in organic synthesis for fluorescent dyes. Fluorescents are a fairly new and very heavily used class of organics. These materials have many applications, as a penetrant liquid for crack detection, synthetic resins, plastics, printing inks, non-destructive testing and sports ball dyeing.

Originality/value

The aim value of this review is to define the scope and limitation of microwave synthesis procedures for the synthesis of novel fluorescent dyes via a simple and economic way.