bluuebunny/crossref_metadata_2025_split huggingface dataset:
Milk progesterone enzyme-linked immunosorbent assay as a tool to investigate ovarian cyclicity of water buffaloes in relation to body condition score and milk production
Authors: Banu Turgish A , Shamsuddin Mohammed , Bhattacharjee Jayonta , Islam Mohammad F , Khan Saiful I , Ahmed Jalal U 
Published: May 2012

Abstract

Background
Application of assisted reproductive technologies in buffaloes is limited to some extent by farmers’ inability to detect oestrus because of its poor expression. The present study aimed at investigating reliability of a milk progesterone enzyme-linked immunosorbent assay (ELISA) to assess the ovarian cyclicity during post partum, oestrus and post-breeding periods in water buffaloes.

Methods
Progesterone concentrations were measured by an ELISA in milk of 23 postpartum buffaloes in relation to oestrus, pregnancy, body condition score (BCS) and milk production. Two milk samples were taken at 10 days intervals, every month starting from day 30 and continued to day 150 post partum. BCS and milk production were recorded during sample collection. Milk samples from bred buffaloes were collected at Day 0 (day of breeding), Days 10–12 and Days 22–24. Defatted milk was preserved at −80°C until analysis. Pregnancy was confirmed by palpation per rectum on Days 70–90.

Results
Seventeen buffaloes had 47 ovulatory cycles, one to four in each, 13 were detected in oestrus once (28 % oestrus detection rate). Progesterone concentration ≥1 ng/ml in one of the two 10-day-interval milk samples reflected ovulation and corpus luteum formation. The intervals between calving to first luteal activity and to first detected oestrus varied from 41 to 123 days (n = 17) and 83 to 135 (n = 13) days, respectively. Eight buffaloes were bred in the course of the study and seven were found pregnant. These buffaloes had a progesterone profile of low (<1 ng/ml), high (≥ 1 ng/ml) and high (≥ 1 ng/ml) on Day 0, Days 10–12 and Days 22–24, respectively. Buffaloes cycling later in the postpartum period had fewer missed oestruses (P < 0.05). Buffaloes with a superior BCS had a shorter calving to oestrus interval and produced more milk (P < 0.05).

Conclusions
Milk progesterone ELISA is a reliable tool for monitoring ovarian cyclicity and good BCS may be an indicator of resuming cyclicity in water buffalo.
Robustness from flexibility in the fungal circadian clock
Authors: Akman Ozgur E , Rand David A , Brown Paul E , Millar Andrew J 
Published: May 2012

Abstract

Background
Robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. A key challenge is to identify the structures in biological circuits that confer system-level properties such as robustness. Circadian clocks allow organisms to adapt to the predictable changes of the 24-hour day/night cycle by generating endogenous rhythms that can be entrained to the external cycle. In all organisms, the clock circuits typically comprise multiple interlocked feedback loops controlling the rhythmic expression of key genes. Previously, we showed that such architectures increase the flexibility of the clock's rhythmic behaviour. We now test the relationship between flexibility and robustness, using a mathematical model of the circuit controlling conidiation in the fungus Neurospora crassa.

Results
The circuit modelled in this work consists of a central negative feedback loop, in which the frequency (frq) gene inhibits its transcriptional activator white collar-1 (wc-1), interlocked with a positive feedback loop in which FRQ protein upregulates WC-1 production. Importantly, our model reproduces the observed entrainment of this circuit under light/dark cycles with varying photoperiod and cycle duration. Our simulations show that whilst the level of frq mRNA is driven directly by the light input, the falling phase of FRQ protein, a molecular correlate of conidiation, maintains a constant phase that is uncoupled from the times of dawn and dusk. The model predicts the behaviour of mutants that uncouple WC-1 production from FRQ's positive feedback, and shows that the positive loop enhances the buffering of conidiation phase against seasonal photoperiod changes. This property is quantified using Kitano's measure for the overall robustness of a regulated system output. Further analysis demonstrates that this functional robustness is a consequence of the greater evolutionary flexibility conferred on the circuit by the interlocking loop structure.

Conclusions
Our model shows that the behaviour of the fungal clock in light-dark cycles can be accounted for by a transcription-translation feedback model of the central FRQ-WC oscillator. More generally, we provide an example of a biological circuit in which greater flexibility yields improved robustness, while also introducing novel sensitivity analysis techniques applicable to a broader range of cellular oscillators.
Stress-specific response of the p53-Mdm2 feedback loop
Authors: Hunziker Alexander , Jensen Mogens H , Krishna Sandeep 
Published: May 2012

Abstract

Background
The p53 signalling pathway has hundreds of inputs and outputs. It can trigger cellular senescence, cell-cycle arrest and apoptosis in response to diverse stress conditions, including DNA damage, hypoxia and nutrient deprivation. Signals from all these inputs are channeled through a single node, the transcription factor p53. Yet, the pathway is flexible enough to produce different downstream gene expression patterns in response to different stresses.

Results
We construct a mathematical model of the negative feedback loop involving p53 and its inhibitor, Mdm2, at the core of this pathway, and use it to examine the effect of different stresses that trigger p53. In response to DNA damage, hypoxia, etc., the model exhibits a wide variety of specific output behaviour - steady states with low or high levels of p53 and Mdm2, as well as spiky oscillations with low or high average p53 levels.

Conclusions
We show that even a simple negative feedback loop is capable of exhibiting the kind of flexible stress-specific response observed in the p53 system. Further, our model provides a framework for predicting the differences in p53 response to different stresses and single nucleotide polymorphisms.
Molecular cytogenetic characterization of undifferentiated embryonal sarcoma of the liver: a case report and literature review
Authors: Hu Xiaoxia , Chen Haiying , Jin Meishan , Wang Xianfu , Lee Jiyun , Xu Weihong , Zhang Rui , Li Shibo , Niu Junqi 
Published: May 2012

AbstractUndifferentiated embryonal sarcoma of the liver (UESL) represents a heterogeneous group of tumors derived from mesenchymal tissues. Earlier cytogenetic studies in limited cases demonstrated that UESL is associated with a recurrent translocation t(11;19)(q11;q13.3-q13.4) or add(19)(q13.4). In this report, we present our array comparative genomic hybridization (aCGH), fluorescencein situhybridization (FISH) findings, and a missense mutation ofTP53gene by DNA sequencing in a 19-year-old patient with UESL. The data were compared to laboratory findings reported by previous studies.
The prognostic value of left ventricular systolic function measured by tissue Doppler imaging in septic shock
Authors: Weng Li , Liu Yong-tai , Du Bin , Zhou Jian-fang , Guo Xiao-xiao , Peng Jin-min , Hu Xiao-yun , Zhang Shu-yang , Fang Quan , Zhu Wen-ling 
Published: May 2012

Abstract
Introduction
Left ventricular (LV) dysfunction is common in septic shock. Its association with the clinical outcome is still controversial. Tissue Doppler imaging (TDI) is a useful tool to quantify LV function; however, little knowledge is available about the prognostic value of these TDI variables in septic shock. Therefore, we performed this prospective study to determine the role of TDI variables in septic shock.

Methods
Patients with septic shock in a medical intensive care unit were studied with transthoracic echocardiography with TDI within 24 hours after the onset of septic shock. Baseline clinical, laboratory, and echocardiographic variables were prospectively collected. Independent predictors of 90-day mortality were analyzed with the Cox regression model.

Results
During a 20-month period, 61 patients were enrolled in the study. The 90-day mortality rate was 39%; the mean APACHE IV score was 84 (68 to 97). Compared with survivors, nonsurvivors exhibited significantly higher peak systolic velocity measured at the mitral annulus (Sa) (11.0 (9.1 to 12.5) versus 7.8 (5.5 to 9.0) cm/sec; P < 0.0001), lower PaO2/FiO2 (123 (83 to 187) versus 186 (142 to 269) mm Hg; P = 0.002], higher heart rate (120 (90 to 140) versus 103 (90 to 114) beats/min; P = 0.004], and ahigher dose of norepinephrine (0.6 (0.2 to 1.0) versus 0.3 (0.2 to 0.5) μg/kg/min; P = 0.007]. In the multivariate analysis, Sa > 9 cm/sec (hazard ratio (HR), 5.559; 95% confidence interval (CI), 2.160 to 14.305; P < 0.0001), dose of norepinephrine (HR, 1.964; 95% CI, 1.338 to 2.883; P = 0.001), and PaO2/FiO2 (HR, 0.992; 95% CI, 0.984 to 0.999; P = 0.031) remain independent predictors of 90-day mortality in septic-shock patients.

Conclusions
Our study demonstrated that LV systolic function as determined by TDI, in particular, Sa, might be associated with mortality in patients with septic shock.
BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair
Authors: Chapman J. Ross , Sossick Alex J. , Boulton Simon J. , Jackson Stephen P. 
Published: May 2012

Summary
Following irradiation, numerous DNA-damage-responsive proteins rapidly redistribute into microscopically visible subnuclear aggregates, termed ionising-radiation-induced foci (IRIF). How the enrichment of proteins on damaged chromatin actually relates to DNA repair remains unclear. Here, we use super-resolution microscopy to examine the spatial distribution of BRCA1 and 53BP1 proteins within single IRIF at subdiffraction-limit resolution, yielding an unprecedented increase in detail that was not previously apparent by conventional microscopy. Consistent with a role for 53BP1 in promoting DNA double-strand break repair by non-homologous end joining, 53BP1 enrichment in IRIF is most prominent in the G0/G1 cell cycle phases, where it is enriched in dense globular structures. By contrast, as cells transition through S phase, the recruitment of BRCA1 into the core of IRIF is associated with an exclusion of 53BP1 to the focal periphery, leading to an overall reduction of 53BP1 occupancy at DNA damage sites. Our data suggest that the BRCA1-associated IRIF core corresponds to chromatin regions associated with repair by homologous recombination, and the enrichment of BRCA1 in IRIF represents a temporal switch in the DNA repair program. We propose that BRCA1 antagonises 53BP1-dependent DNA repair in S phase by inhibiting its interaction with chromatin proximal to damage sites. Furthermore, the genomic instability exhibited by BRCA1-deficient cells might result from a failure to efficiently exclude 53BP1 from such regions during S phase.
Temporal, structural, and pragmatic synchrony between intonation and gesture
Authors: Loehr Daniel P. 
Published: May 2012

AbstractThis paper explores the interaction between intonation and gesture, noting temporal, structural, and pragmatic synchrony. Videotapes of subjects conversing freely were annotated for intonation according to ToBI (Beckman and Elam 1997), and for gesture according to Kendon (1980) and McNeill (1992). The time-stamped annotations were analyzed statistically, as well as visually in the Anvil tool (Kipp 2001), which allows time-aligned viewing of videos with their annotations. Alignments were investigated between three levels of intonational units and four levels of gestural units. The intonational units were, from smallest to largest, pitch accents, intermediate phrases, and intonational phrases. The gestural units, again from smallest to largest, were apices of strokes, gesture phases, gesture phrases, and gesture units. Of these possible combinations, two pairs aligned. Apices clearly aligned with pitch accents, and gesture phrases tended to align with intermediate phrases. The existence of intermediate phrases in English has been the subject of some debate (Ladd 2008), and this paper suggests that a probable gestural correlate to intermediate phrases provides independent evidence for their existence. In addition, intonation and gesture were found to perform simultaneous complementary pragmatic functions. This temporal, structural, and pragmatic synchrony between the two channels reinforces the claim that speech and gesture are two surface forms of the same underlying and emerging cognitive content.
Here's looking at you, baby: What gaze and movement reveal about minimal pair word-object association at 14 months
Authors: Fais Laurel , Werker Janet F. , Cass Bronwyn , Leibowich Julia , Barbosa Adriano Vilela , Vatikiotis-Bateson Eric 
Published: May 2012

AbstractThe ability, or lack thereof, of 14-month-old infants to associate novel, minimal pair word-forms with novel objects in a variety of experimental settings has been a crucial research window into how infants go about the quintessential linguistic task of learning words. Here we ask whether the presence of a human interactor in the experimental setting facilitates minimal pair word-object association at this age. In addition to standard looking time measures to test this question, we also introduce the use of measures of infant movement derived by the application of an efficient algorithm that measures motion from 2D video. Infant gaze patterns across the experimental session identified two groups of infants, those engaging in more and those engaging in less mutual gaze with the Experimenter; both groups demonstrated success in the task by both looking time and movement measures. Infants did not succeed in the task by either measure when a videotaped Experimenter presented the labels. We suggest that infants at this age are in transition from being good “information consumers” to becoming good “information seekers,” and that the presence of the live Experimenter plays a crucial role in making it possible for infants to demonstrate their nascent word learning abilities. Further, we explore insights into the looking time results provided by the movement measures as well as novel contributions to our understanding of language acquisition afforded by the examination of infant movement.
Vowel acoustics reliably differentiate three coronal stops of Wubuy across prosodic contexts
Authors: Bundgaard-Nielsen Rikke L. , Baker Brett J. , Kroos Christian , Harvey Mark , Best Catherine T. 
Published: May 2012

AbstractThe present study investigates the acoustic differentiation of three coronal stops in the indigenous Australian language Wubuy. We test independent claims that only VC (vowel-into-consonant) transitions provide robust acoustic cues for retroflex as compared to alveolar and dental coronal stops, with no differentiating cues among these three coronal stops evident in CV (consonant-into-vowel) transitions. The four-way stop distinction /t, t̪, ʈ, c/ in Wubuy is contrastive word-initially (Heath 1984) and by implication utterance-initially, i.e., in CV-only contexts, which suggests that acoustic differentiation should be expected to occur in the CV transitions of this language, including in initial positions. Therefore, we examined both VC and CV formant transition information in the three target coronal stops across VCV (word-internal), V#CV (word-initial but utterance-medial) and ##CV (word- and utterance-initial), for /а/ vowel contexts, which provide the optimal environment for investigating formant transitions. Results confirm that these coronal contrasts are maintained in the CVs in this vowel context, and in all three positions. The patterns of acoustic differences across the three syllable contexts also provide some support for a systematic role of prosodic boundaries in influencing the degree of coronal stop differentiation evident in the vowel formant transitions.
New and Redesigned pRS Plasmid Shuttle Vectors for Genetic Manipulation of Saccharomyces cerevisiae
Authors: Chee Mark K , Haase Steven B 
Published: May 2012

Abstract
We have constructed a set of 42 plasmid shuttle vectors based on the widely used pRS series for use in the budding yeast Saccharomyces cerevisiae and the bacterium Escherichia coli. This set of pRSII plasmids includes new shuttle vectors that can be used with histidine and adenine auxotrophic laboratory yeast strains carrying mutations in the genes HIS2 and ADE1, respectively. Our pRSII plasmids also include updated versions of commonly used pRS plasmids from which common restriction sites that occur within their yeast-selectable biosynthetic marker genes have been removed to increase the availability of unique restriction sites within their polylinker regions. Hence, our pRSII plasmids are a complete set of integrating, centromere and 2μ episomal plasmids with the biosynthetic marker genes ADE2, HIS3, TRP1, LEU2, URA3, HIS2, and ADE1 and a standardized selection of at least 16 unique restriction sites in their polylinkers. Additionally, we have expanded the range of drug selection options that can be used for PCR-mediated homologous replacement using pRS plasmid templates by replacing the G418-resistance kanMX4 cassette of pRS400 with MX4 cassettes encoding resistance to phleomycin, hygromycin B, nourseothricin, and bialaphos. Finally, in the process of generating the new plasmids, we have determined several errors in existing publicly available sequences for several commonly used yeast plasmids. Using our updated sequences, we constructed pRS plasmid backbones with a unique restriction site for inserting new markers to facilitate future expansion of the pRS series.
Simplified Insertion of Transgenes Onto Balancer Chromosomes via Recombinase-Mediated Cassette Exchange
Authors: Sun Florence F , Johnson Justine E , Zeidler Martin P , Bateman Jack R 
Published: May 2012

Abstract
Balancer chromosomes are critical tools for Drosophila genetics. Many useful transgenes are inserted onto balancers using a random and inefficient process. Here we describe balancer chromosomes that can be directly targeted with transgenes of interest via recombinase-mediated cassette exchange (RMCE).
Aging Uncouples Heritability and Expression-QTL in Caenorhabditis elegans
Authors: Viñuela Ana , Snoek L Basten , Riksen Joost A G , Kammenga Jan E 
Published: May 2012

Abstract
The number and distribution of gene expression QTL (eQTL) represent the genetic architecture of many complex traits, including common human diseases. We previously reported that the heritable eQTL patterns are highly dynamic with age in an N2 × CB4856 recombinant inbred population of the nematode Caenorhabditis elegans. In particular, we showed that the number of eQTL decreased with age. Here, we investigated the reason for this decrease by combining gene expression profiles at three ages in the wild types N2 and CB4856 with the reported expression profiles of the RIL population. We determined heritability and transgression (when gene expression levels in the RILs are more extreme than the parents) and investigated their relation with eQTL changes with age. Transgressive segregation was widespread but depended on physiological age. The percentage of genes with an eQTL increased with a higher heritability in young worms. However, for old worms this percentage hardly increased. Using a single marker approach, we found that almost 20% of genes with heritability &gt;0.9 had an eQTL in developing worms. Surprisingly, only 10% was found in old worms. Using a multimarker approach, this percentage increased to almost 30% for both age groups. Comparison of the single marker to a multiple marker eQTL mapping indicated that heritable regulation of gene expression becomes more polygenic in aging worms due to multiple loci and possible epistatic interactions. We conclude that linkage studies should account for the relation between increased polygenic regulation and diminished effects at older ages.
Multienvironment Quantitative Trait Loci Analysis for Photosynthate Acquisition, Accumulation, and Remobilization Traits in Common Bean Under Drought Stress
Authors: Asfaw Asrat , Blair Matthew W , Struik Paul C 
Published: May 2012

Abstract
Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance.