bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
Authors: Li Wei , Xu Han , Xiao Tengfei , Cong Le , Love Michael I , Zhang Feng , Irizarry Rafael A , Liu Jun S , Brown Myles , Liu X Shirley 
Published: December 2014

AbstractWe propose the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method for prioritizing single-guide RNAs, genes and pathways in genome-scale CRISPR/Cas9 knockout screens. MAGeCK demonstrates better performance compared with existing methods, identifies both positively and negatively selected genes simultaneously, and reports robust results across different experimental conditions. Using public datasets, MAGeCK identified novel essential genes and pathways, including EGFR in vemurafenib-treated A375 cells harboring a BRAF mutation. MAGeCK also detected cell type-specific essential genes, including BCR and ABL1, in KBM7 cells bearing a BCR-ABL fusion, and IGF1R in HL-60 cells, which depends on the insulin signaling pathway for proliferation.
Down on one knee: soft tissue knee injuries across the lifespan
Authors: Thorlund Jonas B , Culvenor Adam G , Ratzlaff Charles 
Published: December 2014

AbstractJoint injury is a potent risk factor for osteoarthritis, the most important musculoskeletal disease affecting humankind. Yet the population incidence of soft tissue knee injury is not well documented. Using health-care register data from Sweden, Peat and colleagues report that soft tissue knee injuries are common, peak in adolescence and early adulthood, have a second spike in women who are 35 to 49 years old, and continue throughout the lifespan. The study highlights the need for more knowledge on the natural history of knee injuries, their impact on knee osteoarthritis development and progression, and the potential for prevention programs to reduce the incidence of these injuries.
Recent trends and future scope in the protection and comfort of fire-fighters’ personal protective clothing
Authors: Nayak Rajkishore , Houshyar Shadi , Padhye Rajiv 
Published: December 2014

AbstractFire-fighters’ personal protective clothing is the only source of protection for fire-fighters during fire-fighting. The protective clothing should provide adequate protection as well as should be comfortable to wear. The protection and comfort requirements are always the contradicting fact in several protective clothing including fire-fighters’. Appropriate material selection, clothing design and final evaluation of the results play a critical role in predicting the clothing performance and comfort. Several researches have been done on the performance and comfort improvement of fire-fighter’s protective clothing. However, detailed review related to these parameters is not being reported in recent years. In this perspective review, we report the recent trends in the performance and comfort properties of the fire-fighters protective clothing. The clothing design and different materials used to achieve a balance between performance and comfort is illustrated. Various test standards related to the performance and comfort is also being discussed. In addition, the future scopes and challenges while designing tomorrows advanced protective clothing are cited. This would provide a guideline in terms of comfort and performance while developing and designing the fire-fighter protective clothing for different climatic conditions.
Analysis of alkali ultrasonication pretreatment in bioethanol production from cotton gin trash using FT-IR spectroscopy and principal component analysis
Authors: Plácido Jersson , Capareda Sergio 
Published: December 2014

Abstract

Background
Cotton gin trash (CGT) is a lignocellulosic residue that can be used in the production of cellulosic ethanol. In a previous research, the sequential use of ultrasonication, liquid hot water, and ligninolytic enzymes was selected as pretreatment for the production of ethanol from CGT. However, an increment in the ethanol production is necessary. To accomplish that, this research evaluated the effect of pretreating CGT using alkaline ultrasonication before a liquid hot water and ligninolytic enzymes pretreatments for ethanol production. Three NaOH concentrations (5%, 10%, and 15%) were employed for the alkaline ultrasonication. Additionally, this work is one of the first applications of Fourier transform infrared (FT-IR) spectrum and principal component analysis (PCA) as fast methodology to identify the differences in the biomass after different types of pretreatments.

Results
The three concentrations employed for the alkaline ultrasonication pretreatment produced ethanol yields and cellulose conversions higher than the experiment without NaOH. Furthermore, 15% NaOH concentration achieved twofold increment yield versus the treatment without NaOH. The FT-IR spectrum confirmed modifications in the CGT structure in the different pretreatments. PCA was helpful to determine differences between the pretreated and un-pretreated biomass and to evaluate how the CGT structure changed after each treatment.

Conclusions
The combination of alkali ultrasonication hydrolysis, liquid hot water, and ligninolytic enzymes using 15% of NaOH improved 35% the ethanol yield compared with the original treatment. Additionally, we demonstrated the use of PCA to identify the modifications in the biomass structure after different types of pretreatments and conditions.
Human mesenchymal stem cells possess different biological characteristics but do not change their therapeutic potential when cultured in serum free medium
Authors: Wang Youwei , Wu Hehe , Yang Zhouxin , Chi Ying , Meng Lei , Mao Aibin , Yan Shulin , Hu Shanshan , Zhang Jianzhong , Zhang Yun , Yu Wenbo , Ma Yue , Li Tao , Cheng Yan , Wang Yongjuan , Wang Shanshan , Liu Jing , Han Jingwen , Li Caiyun , Liu Li , Xu Jian , Han Zhi Bo , Han Zhong Chao 
Published: December 2014

Abstract
Introduction
Mesenchymal stem cells (MSCs) are widely investigated in clinical researches to treat various diseases. Classic culture medium for MSCs, even for clinical use, contains fetal bovine serum. The serum-containing medium (SCM) seems a major obstacle for MSCs-related therapies due to the risk of contamination of infectious pathogens. Some studies showed that MSCs could be expanded in serum free medium (SFM); however, whether SFM would change the biological characteristics and safety issues of MSCs has not been well answered.

Methods
Human umbilical cord mesenchymal stem cells (hUC-MSCs) were cultured in a chemical defined serum free medium. Growth, multipotency, surface antigen expression, telomerase, immunosuppressive ability, gene expression profile and genomic stability of hUC-MSCs cultured in SFM and SCM were analyzed and compared side by side.

Results
hUC-MSCs propagated more slowly and senesce ultimately in SFM. SFM-expanded hUC-MSCs were different from SCM-expanded hUC-MSCs in growth rate, telomerase, gene expression profile. However, SFM-expanded hUC-MSCs maintained multipotency and the profile of surface antigen which were used to define human MSCs. Both SFM- and SCM-expanded hUC-MSCs gained copy number variation (CNV) in long-term in vitro culture.

Conclusion
hUC-MCSs could be expanded in SFM safely to obtain enough cells for clinical application, meeting the basic criteria for human mesenchymal stem cells. hUC-MSCs cultured in SFM were distinct from hUC-MSCs cultured in SCM, yet they remained therapeutic potentials for future regenerative medicine.
Fas regulates neutrophil lifespan during viral and bacterial infection
Authors: O’Donnell Joanne A , Kennedy Catherine L , Pellegrini Marc , Nowell Cameron J , Zhang Jian-Guo , O’Reilly Lorraine A , Cengia Louise , Dias Stuart , Masters Seth L , Hartland Elizabeth L , Roberts Andrew W , Gerlic Motti , Croker Ben A 
Published: December 2014

Abstract
Neutrophils use Toll-like receptor and IL-18 signaling to reprogram Fas-induced death.
The regulation of neutrophil lifespan is critical for a circumscribed immune response. Neutrophils are sensitive to Fas/CD95 death receptor signaling in vitro, but it is unknown if Fas regulates neutrophil lifespan in vivo. We hypothesized that FasL-expressing CD8+ T cells, which kill antigen-stimulated T cells during chronic viral infection, can also induce neutrophil death in tissues during infection. With the use of LysM-Cre Fasfl/fl mice, which lack Fas expression in macrophages and neutrophils, we show that Fas regulates neutrophil lifespan during lymphocytic choriomeningitis virus (LCMV) infection in the lung, peripheral blood, and spleen. Fas also contributed to the regulation of neutrophil numbers in the colon of Citrobacter rodentium-infected mice. To examine the effects of infection on Fas activation in neutrophils, we primed neutrophils with TLR ligands or IL-18, resulting in ablation of Fas death receptor signaling. These data provide the first in vivo genetic evidence that neutrophil lifespan is controlled by death receptor signaling and provide a mechanism to account for neutrophil resistance to Fas stimulation during infection.
Highly Efficient Cosensitized Plastic-Substrate Dye-Sensitized Solar Cells with Black Dye and Pyridine-Anchor Organic Dye
Authors: Shibayama Naoyuki , Ozawa Hironobu , Ooyama Yousuke , Arakawa Hironori 
Published: December 2014

Abstract
Cosensitized plastic-substrate dye-sensitized solar cells (PDSCs) with Black dye and a pyridine-anchor organic dye (NI5 or YNI-2) have been prepared to improve conversion efficiency. Detailed analysis of light-harvesting efficiency spectra and ATR-IR spectra of the cosensitized TiO2 photoelectrodes revealed that the amount of pyridine anchor dye, which adsorbs to the Lewis acid sites of the TiO2 surface and works as a sensitizer, increased with prolonging the immersion time of the Black-dye-adsorbed TiO2 photoelectrodes into the dye-adsorption solvent of pyridine anchor dye up to 60 min. In addition, these measurements also revealed that the dye aggregation between Black dye and pyridine anchor dye occurred just after immersion, even though the amount of pyridine anchor dye which forms dye aggregation with Black dye is small when the immersion time is shorter than 30 min. The conversion efficiency of the Black-dye-based PDSC was improved by cosensitization with pyridine anchor dyes up tol 30 min immersion, and it decreased largely when the immersion time is extended to 60 min. A conversion efficiency of 8.3% (AM 1.5, 100 mW cm−2), which is the highest conversion efficiency in the PDSCs, could be achieved in the cosensitized PDSC with Black dye and NI5 prepared under the optimized conditions.
Impact of Smoothing on Parameter Estimation in Quantitative DNA Amplification Experiments
Authors: Spiess Andrej-Nikolai , Deutschmann Claudia , Burdukiewicz Michał , Himmelreich Ralf , Klat Katharina , Schierack Peter , Rödiger Stefan 
Published: December 2014

Abstract

BACKGROUND
Quantification cycle (Cq) and amplification efficiency (AE) are parameters mathematically extracted from raw data to characterize quantitative PCR (qPCR) reactions and quantify the copy number in a sample. Little attention has been paid to the effects of preprocessing and the use of smoothing or filtering approaches to compensate for noisy data. Existing algorithms largely are taken for granted, and it is unclear which of the various methods is most informative. We investigated the effect of smoothing and filtering algorithms on amplification curve data.

METHODS
We obtained published high-replicate qPCR data sets from standard block thermocyclers and other cycler platforms and statistically evaluated the impact of smoothing on Cq and AE.

RESULTS
Our results indicate that selected smoothing algorithms affect estimates of Cq and AE considerably. The commonly used moving average filter performed worst in all qPCR scenarios. The Savitzky–Golay smoother, cubic splines, and Whittaker smoother resulted overall in the least bias in our setting and exhibited low sensitivity to differences in qPCR AE, whereas other smoothers, such as running mean, introduced an AE-dependent bias.

CONCLUSIONS
The selection of a smoothing algorithm is an important step in developing data analysis pipelines for real-time PCR experiments. We offer guidelines for selection of an appropriate smoothing algorithm in diagnostic qPCR applications. The findings of our study were implemented in the R packages chipPCR and qpcR as a basis for the implementation of an analytical strategy.
Proteolysis is a confounding factor in the interpretation of faecal calprotectin
Authors: Dumoulin Els N. , Van Biervliet Stephanie , Langlois Michel R. , Delanghe Joris R. 
Published: December 2014

AbstractCalprotectin is a 36 kDa calcium and zinc binding protein. An increased level of calprotectin points towards inflammatory bowel disease. However, the biomarker calprotectin shows 14 potential cleavages sites for trypsin. Next to trypsin, also the presence of its inhibitor αAn in vitro model was created. As calprotectin source, leukocytes were isolated and subsequently lysed (1% Triton X-100) and diluted in faecal matrix. Trypsin digestion was carried out by adding trypsin. Incubation occurred for 24 h or 48 h (37 °C). To study the influence of αIn vitro experiments enabled monitoring of the faecal calprotectin digestion, leading to loss of immunoreactivity. Trypsin activity was a potential confounder in the interpretation of calprotectin, in particular for proximal lesions, where exposure of calprotectin to trypsin is prolonged. Relative calprotectin loss was proportional to the amount of trypsin. Decrease of calprotectin was more pronounced after 48 h of incubation in comparison to 24 h of incubation. Analogue experiments also showed stable calprotectin values after adding αTransit time, trypsin activity and addition of blood as a source of α
miR-126 modulates angiogenic growth parameters of peripheral blood endothelial progenitor cells
Authors: Goerke Sebastian M. , Kiefer Lena S. , Stark G. Björn , Simunovic Filip , Finkenzeller Günter 
Published: December 2014

Abstract
Vascularization plays an important role in tissue engineering applications. It is known that implantation of differentiated endothelial cells or endothelial progenitor cells (EPCs) from cord blood (cbEPCs) gives rise to the formation of a complex functional neovasculature, whereas EPCs isolated from peripheral blood (pbEPCs) have a limited capability to form blood vessels upon implantation. MicroRNA-126 (miR-126) has been shown to have pro-angiogenic effects in vivo. In this study, we investigated whether modulation of miR-126 expression in pbEPCs may alter their angiogenic properties. Gain of function and loss of function experiments revealed that miR-126 has anti-angiogenic effects in pbEPCs. Overexpression of miR-126 resulted in decreased proliferation, migration, invasion and tube formation, while inhibition of miR-126 induced the opposite effects. However, modulation of miR-126 expression did not influence apoptotic susceptibility of pbEPCs. This study provides evidence that inhibition of miR-126 improves angiogenesis-related growth parameters in pbEPCs and may represent a therapeutic option to ameliorate the angiogenic and vasculogenic properties of pbEPCs.
Approximations to the full description of stacking disorder in ice I for powder diffraction
Authors: Hansen Thomas C. , Sippel Christian , Kuhs Werner F. 
Published: December 2014

Abstract
Different descriptions of the stacking disorder of the so-called “cubic” phase “ice Ic” and stacking-faulted hexagonal ice Ih exist. We present an overview of the effect of different stacking disorder interaction ranges s from s = 2 to s = 4 after Jagodzinski on the (neutron) powder diffraction patterns of stacking-disordered ice I, which we propose to name ice Ich. We fit in a systematic approach simulated diffraction data of ice Ich for s up to 4 with a multi-peak approach. In this way we allow for estimating the relative proportion of cubic sequences in the stacking sequences by using readily accessible observables of a diffraction pattern.
Ternary stannides RE
2Au5Sn2 (RE = Gd-Er) – i3 superstructures of the Fe2P type
Authors: Fickenscher Thomas , Rodewald Ute Ch. , Pöttgen Rainer 
Published: December 2014

Abstract
The stannides RE
2Au5Sn2 (RE = Gd-Er) were synthesized by arc-melting of the elements and subsequent annealing in tantalum crucibles in sealed evacuated silica tubes. The samples were characterized by powder X-ray diffraction and two structures were refined on the basis of single-crystal X-ray diffractometer data: ordered Au7Ga2 variant,

P

6
¯

2
m
,

$P\bar 62m,$

a = 820.14(4), c = 942.72(5) pm, wR2 = 0.0798, 789 F
2 values, 34 variables for Tb2Au4.70Sn2.30 and a = 816.1(1), c = 941.3(2) pm, wR2 = 0.0600, 723 F
2 values, 35 variables for Er2Au5.03Sn1.91. All stannides exhibit small homogeneity ranges resulting from Au/Sn mixing and/or defects within the tin substructure. The RE
2Au5Sn2 structures derive from the aristotype ZrNiAl (ordered version of Fe2P) by a group-subgroup relation (isomorphic transition of index 3). The crystal chemical details are discussed in comparison with the ZrNiAl type stannide CeRhSn which crystallizes with the subcell structure.
Zur Reform des französischen Kartellrechts
Authors: Stockmann Kurt 
Published: December 2014

Zusammenfassung
Das französische Kartellrecht ist im Jahre 2008 in einer Reihe von Punkten tiefgreifend reformieret worden. Zu den Hauptpunkten der Reform gehörte vor allem die Einrichtung einer neuen, unabhängigen und mit umfassenden Kompetenzen ausgestatteten Kartellbehörde, der Autorité de la concurrence. Ein weiterer Schwerpunkt der Reform betraf die Zusammenschlusskontrolle, die weitgehend der neuen Kartellbehörde übertragen wurde. Die seit der Reform vergangene Zeit erlaubt Rückschlüsse auf ihren Erfolg.
Die Angebotssubstituierbarkeit in der Marktabgrenzung
Authors: Dreher Meinrad , Thomas Stefan 
Published: December 2014

Zusammenfassung
Bei der Abgrenzung von Angebotsmärkten steht das Konzept der Nachfragesubstituierbarkeit im Vordergrund, das auch als Bedarfsmarktkonzept bezeichnet wird. Weniger Beachtung findet vielfach die Erkenntnis, dass die Grenzen des relevanten Marktes ferner durch die Angebotsumstellungsflexibilität von Unternehmen bestimmt werden, was zu dem Konzept der Angebotssubstituierbarkeit führt. Zwar ist die Prüfung von Angebotsumstellungsflexibilitäten bei der Marktabgrenzung durch die EU-Kommission sowie die deutschen Kartellbehörden und die Gerichte im Grundsatz anerkannt. Die Entscheidungspraxis insgesamt trägt dem aber nicht immer hinreichend Rechnung. Das Konzept wird teilweise ohne nähere Begründung überhaupt nicht erörtert, in anderen Fällen lediglich oberflächlich herangezogen. Auch die Voraussetzungen und Maßstäbe für eine relevante Angebotsumstellungsflexibilität sind in der Entscheidungspraxis weniger durchdrungen, als dies für das Bedarfsmarktkonzept gilt. Daher besteht Anlass, die Entscheidungspraxis zur Angebotsumstellungsflexibilität zu hinterfragen.
„Signalling“ und das Kartellverbot – öffentliche Verlautbarungen im Fokus der Kartellbehörden
Authors: Pahlen Robert , Vahrenholt Oliver 
Published: December 2014

Zusammenfassung
Seit der „Wood pulp“-Entscheidung der Europäischen Kommission von 1984 und dem dieser Entscheidung nachfolgenden Urteil des EuGH aus dem Jahre 1993 waren öffentliche Verlautbarungen wie Preis- und Mengenankündigungen als möglicher Kartellverstoß mit wenigen Ausnahmen eher ein theoretischer Aspekt der Kartellrechtspraxis. In der jüngeren Vergangenheit hat das Thema jedoch an neuer Dynamik gewonnen. Dies ist auf eine Reihe von Verfahren zurückzuführen, welche von nationalen Kartellbehörden und der Europäischen Kommission geführt wurden bzw. noch geführt werden. Zwar gibt es bisher keine rechtskräftige Entscheidung, doch die Nachricht ist eindeutig: Das sog. „Signalling“, also öffentliche Verlautbarungen über zukünftiges Marktverhalten, ist stärker in den Ermittlungsfokus der Wettbewerbsbehörden gerückt. Die Unsicherheit bei den Unternehmen ist groß – was ist noch zulässig und bloßes Parallelverhalten, was ist schon eine Verhaltensabstimmung und somit nicht mehr erlaubt? Oftmals erfüllen die öffentlichen Verlautbarungen nämlich legitime Geschäftsfunktionen. Der Kartellrechtspraxis fehlen aber klare Leitlinien zur Bewertung der Fallgruppe des „Signalling“. Der vorliegende Artikel erarbeitet auf rechtlicher und ökonomischer Basis ein Konzept zur eindeutigen Identifizierung zulässiger und unzulässiger Verhaltensweisen.
Influence of illness and unhealthy behavior on health‐related early retirement in Korea: Results from a longitudinal study in Korea
Authors: Kang Mo‐Yeol , Yoon Chang‐gyo , Yoon Jin‐Ha 
Published: December 2014

Influence of illness and unhealthy behavior on health‐related early retirement in Korea: Results from a longitudinal study in Korea: Mo‐Yeol KANG, et al. Institute for Occupational and Environmental Health, Wonjin Green Hospital, Republic of Korea—ObjectivesThe aim of this study was to elucidate the effect of illness and unhealthy behavior on early retirement due to health problems (ERdHP) using Korean longitudinal data.MethodsThis study used data collected from 3,508 subjects enrolled in the first to fourth phases of the Korean Longitudinal Study of Ageing (KLoSA). This study was conducted from 2006 to 2012 using structured questionnaires on retirement, morbidities, and health‐related behaviors. We adopted the Cox proportional hazard model to investigate the effects of diagnosed disease and health‐related behaviors on ERdHP.ResultsParticipants who smoked, were obese, or suffered from hypertension, diabetes, malignancy, heart disease, stroke, or arthritis had a significantly higher risk of health‐related early retirement after adjustment for gender, age, and occupation. Further, risk factors such as lack of exercise, stroke, arthritis, obesity, and malignancy differentially affect early retirement by gender.ConclusionsThis is the first study, that we are aware of, to examine the effect of illness and unhealthy behavior on ERdHP in Asia, using Korean longitudinal data. We found that hypertension, diabetes, malignancy, arthritis, cardiovascular and cerebrovascular diseases, smoking, and obesity increased the risk of ERdHP. To enhance the sustainability of labor in an aging society, more studies on ERdHP are needed.