bluuebunny/crossref_metadata_2025_split huggingface dataset:
New insights into lineage restriction of mammary gland epithelium using parity-identified mammary epithelial cells
Authors: Chang Ted H-T , Kunasegaran Kamini , Tarulli Gerard A , De Silva Duvini , Voorhoeve P Mathijs , Pietersen Alexandra M 
Published: January 2014

Abstract
Introduction
Parity-identified mammary epithelial cells (PI-MECs) are an interesting cellular subset because they survive involution and are a presumptive target for transformation by human epidermal growth factor receptor 2 (HER2)/neu in mammary tumors. Depending on the type of assay, PI-MECs have been designated lobule-restricted progenitors or multipotent stem/progenitor cells. PI-MECs were reported to be part of the basal population of mammary epithelium based on flow cytometry. We investigated the cellular identity and lineage potential of PI-MECs in intact mammary glands.

Methods
We performed a quantitative and qualitative analysis of the contribution of PI-MECs to mammary epithelial cell lineages in pregnant and involuted mammary glands by immunohistochemistry, fluorescence-activated cells sorting (FACS), and quantitative polymerase chain reaction. PI-MECs were labeled by the activation of Whey Acidic Protein (WAP)-Cre during pregnancy that results in permanent expression of yellow fluorescent protein.

Results
After involution, PI-MECs are present exclusively in the luminal layer of mammary ducts. During pregnancy, PI-MECs contribute to the luminal layer but not the basal layer of alveolar lobules. Strikingly, whereas all luminal estrogen receptor (ER)-negative cells in an alveolus can be derived from PI-MECs, the alveolar ER-positive cells are unlabeled and reminiscent of Notch2-traced L cells. Notably, we observed a significant population of unlabeled alveolar progenitors that resemble PI-MECs based on transcriptional and histological analysis.

Conclusions
Our demonstration that PI-MECs are luminal cells underscores that not only basal cells display multi-lineage potential in transplantation assays. However, the lineage potential of PI-MECs in unperturbed mammary glands is remarkably restricted to luminal ER-negative cells of the secretory alveolar lineage. The identification of an unlabeled but functionally similar population of luminal alveolar progenitor cells raises the question of whether PI-MECs are a unique population or the result of stochastic labeling. Interestingly, even when all luminal ER-negative cells of an alveolus are PI-MEC-derived, the basal cells and hormone-sensing cells are derived from a different source, indicating that cooperative outgrowth of cells from different lineages is common in alveologenesis.
Presepsin (soluble CD14 subtype) and procalcitonin levels for mortality prediction in sepsis: data from the Albumin Italian Outcome Sepsis trial
Authors: Masson Serge , Caironi Pietro , Spanuth Eberhard , Thomae Ralf , Panigada Mauro , Sangiorgi Gabriela , Fumagalli Roberto , Mauri Tommaso , Isgrò Stefano , Fanizza Caterina , Romero Marilena , Tognoni Gianni , Latini Roberto , Gattinoni Luciano 
Published: January 2014

Abstract
Introduction
Sepsis, a leading cause of death in critically ill patients, is the result of complex interactions between the infecting microorganisms and the host responses that influence clinical outcomes. We evaluated the prognostic value of presepsin (sCD14-ST), a novel biomarker of bacterial infection, and compared it with procalcitonin (PCT).

Methods
This is a retrospective, case–control study of a multicenter, randomized clinical trial enrolling patients with severe sepsis or septic shock in ICUs in Italy. We selected 50 survivors and 50 non-survivors at ICU discharge, matched for age, sex and time from sepsis diagnosis to enrollment. Plasma samples were collected 1, 2 and 7 days after enrollment to assay presepsin and PCT. Outcome was assessed 28 and 90 days after enrollment.

Results
Early presepsin (day 1) was higher in decedents (2,269 pg/ml, median (Q1 to Q3), 1,171 to 4,300 pg/ml) than in survivors (1,184 pg/ml (median, 875 to 2,113); P = 0.002), whereas PCT was not different (18.5 μg/L (median 3.4 to 45.2) and 10.8 μg/L (2.7 to 41.9); P = 0.31). The evolution of presepsin levels over time was significantly different in survivors compared to decedents (P for time-survival interaction = 0.03), whereas PCT decreased similarly in the two groups (P = 0.13). Presepsin was the only variable independently associated with ICU and 28-day mortality in Cox models adjusted for clinical characteristics. It showed better prognostic accuracy than PCT in the range of Sequential Organ Failure Assessment score (area under the curve (AUC) from 0.64 to 0.75 vs. AUC 0.53 to 0.65).

Conclusions
In this multicenter clinical trial, we provide the first evidence that presepsin measurements may have useful prognostic information for patients with severe sepsis or septic shock. These preliminary findings suggest that presepsin may be of clinical importance for early risk stratification.
Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
Authors: Cui Peng , Zhang Shoudong , Ding Feng , Ali Shahjahan , Xiong Liming 
Published: January 2014

Abstract
Background
Sm-like proteins are highly conserved proteins that form the core of the U6 ribonucleoprotein and function in several mRNA metabolism processes, including pre-mRNA splicing. Despite their wide occurrence in all eukaryotes, little is known about the roles of Sm-like proteins in the regulation of splicing.

Results
Here, through comprehensive transcriptome analyses, we demonstrate that depletion of the Arabidopsis supersensitive to abscisic acid and drought 1 gene (SAD1), which encodes Sm-like protein 5 (LSm5), promotes an inaccurate selection of splice sites that leads to a genome-wide increase in alternative splicing. In contrast, overexpression of SAD1 strengthens the precision of splice-site recognition and globally inhibits alternative splicing. Further, SAD1 modulates the splicing of stress-responsive genes, particularly under salt-stress conditions. Finally, we find that overexpression of SAD1 in Arabidopsis improves salt tolerance in transgenic plants, which correlates with an increase in splicing accuracy and efficiency for stress-responsive genes.

Conclusions
We conclude that SAD1 dynamically controls splicing efficiency and splice-site recognition in Arabidopsis, and propose that this may contribute to SAD1-mediated stress tolerance through the metabolism of transcripts expressed from stress-responsive genes. Our study not only provides novel insights into the function of Sm-like proteins in splicing, but also uncovers new means to improve splicing efficiency and to enhance stress tolerance in a higher eukaryote.
Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens
Authors: Wu Hshin-Ping , Su Yi-shin , Chen Hsiu-Chen , Chen Yu-Rong , Wu Chia-Chen , Lin Wen-Dar , Tu Shih-Long 
Published: January 2014

Abstract
Background
Light is one of the most important factors regulating plant growth and development. Light-sensing photoreceptors tightly regulate gene expression to control photomorphogenic responses. Although many levels of gene expression are modulated by photoreceptors, regulation at the mRNA splicing step remains unclear.

Results
We performed high-throughput mRNA sequencing to analyze light-responsive changes in alternative splicing in the moss Physcomitrella patens, and found that a large number of alternative splicing events were induced by light in the moss protonema. Light-responsive intron retention preferentially occurred in transcripts involved in photosynthesis and translation. Many of the alternatively spliced transcripts were expressed from genes with a function relating to splicing or light signaling, suggesting a potential impact on pre-mRNA splicing and photomorphogenic gene regulation in response to light. Moreover, most light-regulated intron retention was induced immediately upon light exposure, while motif analysis identified a repetitive GAA motif that may function as an exonic regulatory cis element in light-mediated alternative splicing. Further analysis in gene-disrupted mutants was consistent with a function for multiple red-light photoreceptors in the upstream regulation of light-responsive alternative splicing.

Conclusions
Our results indicate that intensive alternative splicing occurs in non-vascular plants and that, during photomorphogenesis, light regulates alternative splicing with transcript selectivity. We further suggest that alternative splicing is rapidly fine-tuned by light to modulate gene expression and reorganize metabolic processes, and that pre-mRNA cis elements are involved in photoreceptor-mediated splicing regulation.
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Authors: Webb Shaun , Hector Ralph D , Kudla Grzegorz , Granneman Sander 
Published: January 2014

Abstract
Background
Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA coding genes; however, it remains unclear exactly what percentage of the mRNA component of the transcriptome these proteins control. To address this question, we used the pyCRAC software package developed in our laboratory to analyze CRAC and PAR-CLIP data for Nrd1-Nab3-RNA interactions.

Results
We generated high-resolution maps of Nrd1-Nab3-RNA interactions, from which we have uncovered hundreds of new Nrd1-Nab3 mRNA targets, representing between 20 and 30% of protein-coding transcripts. Although Nrd1 and Nab3 showed a preference for binding near 5′ ends of relatively short transcripts, they bound transcripts throughout coding sequences and 3′ UTRs. Moreover, our data for Nrd1-Nab3 binding to 3′ UTRs was consistent with a role for these proteins in the termination of transcription. Our data also support a tight integration of Nrd1-Nab3 with the nutrient response pathway. Finally, we provide experimental evidence for some of our predictions, using northern blot and RT-PCR assays.

Conclusions
Collectively, our data support the notion that Nrd1 and Nab3 function is tightly integrated with the nutrient response and indicate a role for these proteins in the regulation of many mRNA coding genes. Further, we provide evidence to support the hypothesis that Nrd1-Nab3 represents a failsafe termination mechanism in instances of readthrough transcription.
Mindfulness-Based Stress Reduction Compared With Cognitive Behavioral Therapy for the Treatment of Insomnia Comorbid With Cancer: A Randomized, Partially Blinded, Noninferiority Trial
Authors: Garland Sheila N. , Carlson Linda E. , Stephens Alisa J. , Antle Michael C. , Samuels Charles , Campbell Tavis S. 
Published: January 2014

Purpose Our study examined whether mindfulness-based stress reduction (MBSR) is noninferior to cognitive behavioral therapy for insomnia (CBT-I) for the treatment of insomnia in patients with cancer. Patients and Methods This was a randomized, partially blinded, noninferiority trial involving patients with cancer with insomnia recruited from a tertiary cancer center in Calgary, Alberta, Canada, from September 2008 to March 2011. Assessments were conducted at baseline, after the program, and after 3 months of follow-up. The noninferiority margin was 4 points measured by the Insomnia Severity Index. Sleep diaries and actigraphy measured sleep onset latency (SOL), wake after sleep onset (WASO), total sleep time (TST), and sleep efficiency. Secondary outcomes included sleep quality, sleep beliefs, mood, and stress. Results Of 327 patients screened, 111 were randomly assigned (CBT-I, n = 47; MBSR, n = 64). MBSR was inferior to CBT-I for improving insomnia severity immediately after the program (P = .35), but MBSR demonstrated noninferiority at follow-up (P = .02). Sleep diary–measured SOL was reduced by 22 minutes in the CBT-I group and by 14 minutes in the MBSR group at follow-up. Similar reductions in WASO were observed for both groups. TST increased by 0.60 hours for CBT-I and 0.75 hours for MBSR. CBT-I improved sleep quality (P < .001) and dysfunctional sleep beliefs (P < .001), whereas both groups experienced reduced stress (P < .001) and mood disturbance (P < .001). Conclusion Although MBSR produced a clinically significant change in sleep and psychological outcomes, CBT-I was associated with rapid and durable improvement and remains the best choice for the nonpharmacologic treatment of insomnia.
Effectiveness of the Quadrivalent Human Papillomavirus Vaccine Against Cervical Dysplasia in Manitoba, Canada
Authors: Mahmud Salaheddin M. , Kliewer Erich V. , Lambert Pascal , Bozat-Emre Songul , Demers Alain A. 
Published: January 2014

Purpose Effectiveness of the quadrivalent human papillomavirus (QHPV) vaccine against cervical dysplasia has not been estimated using population-based individual level data. We assessed the vaccine effectiveness (VE) of the QHPV vaccine against cervical dysplasia using data collected routinely in Manitoba. Methods Females ≥ 15 years old who received the QHPV vaccine in Manitoba between September 2006 and April 2010 privately (n = 3,541) were matched on age to up to three nonvaccinated females (n = 9,594). We used Cox regression models to estimate the hazard ratios for three outcomes: atypical squamous cells of undetermined significance (ASCUS), low-grade squamous intraepithelial lesions (LSILs), and high-grade SILs (HSILs). Results Among the 15- to 17-year-olds, the adjusted VE estimates were 35% (95% CI, −19% to 65%), 21% (−10% to 43%), and −1% (−44% to 29%) against the detection of HSILs, LSILs, and ASCUS, respectively. The corresponding estimates were higher (46% [0% to 71%], 35% [10% to 54%], and 23% [−8% to 45%]) among those who had ≥ one Pap smear after enrollment. The QHPV vaccine was associated with 23% (−17% to 48%) reduction in HSIL risk among those ≥ 18 with no history of abnormal cytology, but there was no evidence of protection among those with such a history (−8% [−59% to 27%]). Conclusion A significant percentage of vaccinated women may not be protected against HSIL and lesser dysplasia especially if they were vaccinated at older age (≥ 18) or had abnormal cytology before vaccination. These findings affirm the importance of vaccination before any significant exposure to HPV occurs and underscore the need for screening programs that cover all sexually active women, even if they were vaccinated.
Two new Mastogloia species (Bacillariophyceae), M. parlibellioides and M. lyra, from coral reefs in Guam, Western Pacific1
Authors: Lobban Christopher S. , Pennesi Chiara 
Published: January 2014

Abstract
This paper describes the morphology of two new species of Mastogloia identified during a survey of the marine benthic diatom flora of Guam. Mastogloia parlibellioides sp. nov., classified in the section Decussatae, is distinctive in the combination of its valve shape and stria pattern reminiscent of Parlibellus, as well as the presence of rudimentary division walls extending from the free margin to the middle of each partectum. Mastogloia lyra sp. nov., classified in the section Sulcatae, subgroup 2, has internal lyre-shaped lateral sterna and partecta that are displaced toward the midline of the valve by a siliceous flange, which shows oblique partectal ducts. The descriptions of these two new species increase the knowledge base of biodiversity in a Pacific Ocean Mastogloia hotspot.
A reconstruction theorem for abelian categories of twisted sheaves
Authors: Antieau Benjamin 
Published: January 2014

Abstract

We use an idea of Rosenberg to prove a reconstruction theorem for abelian categories of
α-twisted quasi-coherent sheaves on quasi-compact and quasi-separated schemes X when

α
∈
Br
(
X
)

$\alpha \in \operatorname{Br}(X)$

. By applying the work of Toën on derived Azumaya algebras, we give a
proof of Căldăraru's conjecture.
Differential diagnosis: the key to reducing diagnosis error, measuring diagnosis and a mechanism to reduce healthcare costs
Authors: Maude Jason 
Published: January 2014

AbstractDifferential diagnosis has been taught in medical schools for over 100 years and yet it is not routinely carried out in practice; nor is it required to be documented within medical notes. I strongly believe that the routine use of a differential diagnosis would not only substantially reduce the level of diagnostic error but would also greatly reduce the cost of healthcare. This solution to the seemingly intractable problems of diagnostic error and rising healthcare costs is simple and has been with us for 100 years!
Figure and ground in physician misdiagnosis: metacognition and diagnostic norms
Authors: Hamm Robert M. 
Published: January 2014

AbstractMeta-cognitive awareness, or self reflection informed by the “heuristics and biases” theory of how experts make cognitive errors, has been offered as a partial solution for diagnostic errors in medicine. I argue that this approach is not as easy nor as effective as one might hope. We should also promote mastery of the basic principles of diagnosis in medical school, continuing medical education, and routine reflection and review. While it may seem difficult to attend to both levels simultaneously, there is more to be gained from attending to both than from focusing only on one.
Bias: a normal operating characteristic of the diagnosing brain
Authors: Croskerry Pat 
Published: January 2014

AbstractPeople diagnose themselves or receive advice about their illnesses from a variety of sources ranging from their family or friends, alternate medicine, or through conventional medicine. In all cases, the diagnosing mechanism is the human brain which normally operates under the influence of a variety of biases. Most, but not all biases, reside in intuitive decision making, and no individual or group is immune from them. Two biases in particular, bias blind spot and myside bias, have presented obstacles to accepting the impact of bias on medical decision making. Nevertheless, there is now a widespread appreciation of the important role of bias in the majority of medical disciplines. The dual process model of decision making now seems well accepted, although a polarization of opinions has arisen with some arguing the merits of intuitive approaches over analytical ones and vice versa. We should instead accept that it is not one mode or the other that enables well-calibrated thinking but the discriminating use of both. A pivotal role for analytical thinking lies in its ability to allow decision makers the means to detach from the intuitive mode to mitigate bias; it is the gatekeeper for the final diagnostic decision. Exploring and cultivating such debiasing initiatives should be seen as the next major research area in clinical decision making. Awareness of bias and strategies for debiasing are important aspects of the critical thinker’s armamentarium. Promoting critical thinking in undergraduate, postgraduate and continuing medical education will lead to better calibrated diagnosticians.
Expanding the Shopping Cart or Improving Its Contents: A Study on “Modern” Retail in India
Authors: Roy Devesh , Joshi Pramod Kumar , Karandikar Bhushana , Joshi Shwetima , Sonkar Vinay Kumar 
Published: January 2014

Abstract
Several factors (including rising incomes, urbanization, a young population, and more women in the labor force) have influenced retailing in India in recent years, with the emergence and rapid spread of supermarkets being the most dramatic change. Without disputing the high growth rates of organized retail in the food sector, in this study we test whether supermarket growth is associated with greater demand for nonprice attributes such as food safety and customization of products. Using on-site surveys at supermarkets in three Indian cities of different population sizes and income levels, and using ordered models for consumer choice, we find that nonprice attributes remain subordinate to price for consumers in supermarkets. At the same time, rising import penetration in supermarkets creates an outlet where some consumers can satisfy their demand for nonprice attributes that are not provided by domestic products. The fact that such attributes are not demanded of domestic products and that imports fill in to provide these nonprice attributes implies that demand pull for back-end development is weak in Indian food retail. This is important, because a command approach by the government to induce back-end development will work only if enforcement is strong, which seems unlikely.
Conflict-Induced Poverty: Evidence from Colombia
Authors: Lemus Natalia 
Published: January 2014

AbstractColombia is a country with both high incidence of poverty and an ongoing civil conflict. This study uses measures of government deterrence and anti-narcotic activity as instruments of conflict-specific variables to estimate the impact of conflict on poverty in Colombia. Using census-level data at the municipality level for 2005, I assess the effect of conflict on both the urban and rural incidence of the newly developed Multidimensional Poverty Index. The findings show that the incidence of conflict significantly increases rural, but not urban, poverty. This is consistent with the fact that most of the conflict in Colombia takes place in rural areas. I also explore the lagged effect of conflict on poverty to conclude that it lasts for at least 3 years, but decreases over time. Finally, I show that the results are robust to a battery of additional specifications, including the use of alternative conflict data and a modified version of the dependent variable.
Differentiating between Cushing's disease and pseudo-Cushing's syndrome: comparison of four tests
Authors: Alwani R A , Schmit Jongbloed L W , de Jong F H , van der Lely A J , de Herder W W , Feelders R A 
Published: January 2014

ObjectiveTo evaluate the diagnostic performance of four different tests in order to differentiate between Cushing's disease (CD) and pseudo-Cushing's syndrome (PCS).MethodsIn this prospective study, a total of 73 patients with clinical features of hypercortisolism and insufficient suppression of serum cortisol after 1 mg overnight dexamethasone and/or an elevated excretion of cortisol in 24-h urine samples were included. The circadian rhythm of serum cortisol levels as well as midnight serum cortisol (MserC) levels were assessed in all 73 patients. Late-night salivary cortisol (LNSC) concentrations were obtained in 44 patients. The dexamethasone–CRH (Dex–CRH) test was performed in 54 patients.ResultsFifty-three patients were diagnosed with CD and subsequently treated. Twenty patients were classified as having PSC. Serum cortisol circadian rhythm: the diurnal rhythmicity of cortisol secretion was retained in PCS. A cortisol midnight:morning ratio of >0.67 is highly suggestive of CD (positive predictive value (PPV) 100% and negative predictive value (NPV) 73%). MserC concentration >243 nmol/l has a PPV of 98% in predicting true CD (NPV 95%). LNSC level >9.3 nmol/l predicted CD in 94% of patients (NPV 100%). Dex–CRH test: after 2 days of dexamethasone suppression, a CRH-stimulated cortisol level >87 nmol/l (T=15 min) resulted in a PPV of 100% and an NPV of 90%.ConclusionThe Dex–CRH test as well as a single measurement of cortisol in serum or saliva at late (mid-) night demonstrated high diagnostic accuracy in differentiating PCS from true CD.