bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying unusual commits on GitHub
Authors: Goyal Raman , Ferreira Gabriel , Kästner Christian , Herbsleb James 
Published: September 2017

AbstractTransparent environments and social‐coding platforms as GitHub help developers to stay abreast of changes during the development and maintenance phase of a project. Especially, notification feeds can help developers to learn about relevant changes in other projects. Unfortunately, transparent environments can quickly overwhelm developers with too many notifications, such that they lose the important ones in a sea of noise. Complementing existing prioritization and filtering strategies based on binary compatibility and code ownership, we develop an anomaly detection mechanism to identify unusual commits in a repository, which stand out with respect to other changes in the same repository or by the same developer. Among others, we detect exceptionally large commits, commits at unusual times, and commits touching rarely changed file types given the characteristics of a particular repository or developer. We automatically flag unusual commits on GitHub through a browser plug‐in. In an interactive survey with 173 active GitHub users, rating commits in a project of their interest, we found that, although our unusual score is only a weak predictor of whether developers want to be notified about a commit, information about unusual characteristics of a commit changes how developers regard commits. Our anomaly detection mechanism is a building block for scaling transparent environments.
A hindsight reflection on the clinical studies of poly(l‐glutamic acid)‐paclitaxel
Authors: Zhao Jun , Koay Eugene J. , Li Tingting , Wen Xiaoxia , Li Chun 
Published: September 2017

Chemotherapy for cancer treatment is limited by the excessive toxicity to normal tissues. The design of chemodrug‐loaded nanoformulations provides a unique approach to improve the treatment efficacy while minimizing toxicity. Despite the numerous publications of nanomedicine for the last several decades, however, only a small fraction of the developed nanoformulations have entered clinical trials, with even fewer being approved for clinical application. Poly(l‐glutamic acid)‐paclitaxel (PG‐TXL) belongs to the few formulations that reached phase III clinical trials. Unfortunately, the development of PG‐TXL stopped in 2016 due to the inability to show significant improvement over current standard care. This review will provide an overview of the preclinical and clinical evaluations of PG‐TXL, and discuss lessons to be learned from this ordeal. The precise identification of suitable patients for clinical trial studies, deep understanding of the mechanisms of action, and an effective academic‐industry partnership throughout all phases of drug development are important for the successful bench‐to‐bedside translation of new nanoformulations.This article is categorized under:

Implantable Materials and Surgical Technologies > Nanomaterials and Implants
Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease
Biology-Inspired Nanomaterials > Peptide‐Based Structures
The yeasts of the genus Spathaspora: potential candidates for second‐generation biofuel production
Authors: Cadete Raquel M. , Rosa Carlos A. 
Published: September 2017

AbstractYeasts of the Spathaspora clade have the ability to convert d‐xylose to ethanol and/or xylitol. This is an important trait, as these yeasts may be used to produce bioethanol from lignocellulosic biomass or as a source of new d‐xylose metabolism genes for recombinant industrial strains of Saccharomyces cerevisiae. The core group of the genus Spathaspora has 22 species, both formally described and not yet described. Other species, such as Sp. allomyrinae, Candida alai, C. insectamans, C. lyxosophila, C. sake, Sp. boniae and C. subhashii are weakly associated with this clade, based on LSU rRNA gene D1/D2 sequence analyses. Spathaspora passalidarum, Sp. arborariae, Sp. gorwiae and Sp. hagerdaliae produce mostly ethanol from d‐xylose, whereas the remaining species within the Spathaspora clade already tested for this property may be considered xylitol producers. Among the d‐xylose‐fermenting Spathaspora species, Sp. passalidarum is the best ethanol producer, displaying high ethanol yields and productivities when cultured in media supplemented with this pentose under oxygen‐limited or anaerobic conditions. The species also exhibits rapid d‐xylose consumption and the ability to ferment glucose, xylose and cellobiose simultaneously. These characteristics suggest that Sp. passalidarum is a potential candidate for domestication and use in the fermentation of lignocellulosic materials. Copyright © 2017 John Wiley & Sons, Ltd.
Spin-label Order Parameter Calibrations for Slow Motion
Authors: Marsh Derek 
Published: September 2017

Abstract
Calibrations are given to extract orientation order parameters from pseudo-powder electron paramagnetic resonance line shapes of 14N-nitroxide spin labels undergoing slow rotational diffusion. The nitroxide z-axis is assumed parallel to the long molecular axis. Stochastic-Liouville simulations of slow-motion 9.4-GHz spectra for molecular ordering with a Maier–Saupe orientation potential reveal a linear dependence of the splittings,

$$2A_{\hbox{max} }$$

2

A
max

and

$$2A_{\hbox{min} }$$

2

A
min

, of the outer and inner peaks on order parameter

$$S_{zz}$$

S

z
z

that depends on the diffusion coefficient

$$D_{{{\text{R}} \bot }}$$

D

R
⊥

which characterizes fluctuations of the long molecular axis. This results in empirical expressions for order parameter and isotropic hyperfine coupling:

$$S_{zz} = s_{1} \times \left( {A_{\hbox{max} } - A_{\hbox{min} } } \right) - s_{o}$$

S

z
z

=

s
1

×

A
max

-

A
min

-

s
o

and

$$a_{o}^{{}} = \tfrac{1}{3}\left( {f_{\hbox{max} } A_{\hbox{max} } + f_{\hbox{min} } A_{\hbox{min} } } \right) + \delta a_{o}$$

a

o

=

1
3

f
max

A
max

+

f
min

A
min

+
δ

a
o

, respectively. Values of the calibration constants

$$s_{1}$$

s
1

,

$$s_{\text{o}}$$

s
o

,

$$f_{\hbox{max} }$$

f
max

,

$$f_{\hbox{min} }$$

f
min

and

$$\delta a_{o}$$

δ

a
o

are given for different values of

$$D_{{{\text{R}} \bot }}$$

D

R
⊥

in fast and slow motional regimes. The calibrations are relatively insensitive to anisotropy of rotational diffusion

$$(D_{{{\text{R}}//}} \ge D_{{{\text{R}} \bot }} )$$

(

D

R
/
/

≥

D

R
⊥

)

, and corrections are less significant for the isotropic hyperfine coupling than for the order parameter.
Preoperative Valgus Alignment Does Not Predict Inferior Outcome of Total Knee Arthroplasty
Authors: Kahlenberg Cynthia A. , Trivellas Myra , Lee Yuo-yu , Padgett Douglas E. 
Published: September 2017

Background Preoperative valgus deformity is present in an estimated 10–20% of patients undergoing total knee replacement (TKR). Questions/Purposes The objective of this study was to compare the Western Ontario and McMaster Universities Arthritis Index (WOMAC) scores after TKR in a matched cohort of patients with preoperative valgus and varus deformities. Methods This is a matched cohort study of 162 patients with varus native knees and 162 patients with valgus native knees who underwent TKR and were prospectively followed in our institutional registry. Patients matched were based on age, BMI, sex, and severity of preoperative knee deformity, which was classified as mild, moderate, severe varus or valgus, or no deformity. Outcomes were evaluated using the WOMAC preoperatively and at 6 weeks, 3 months, 6 months, and 1 year postoperatively. Results No significant difference was found between the matched varus and valgus cohorts in all WOMAC subdomain scores except for a marginally worse stiffness at 1 year in patients with valgus deformity (WOMAC stiffness, 75.1 varus vs. 70.1 valgus; P = 0.049). This is below the minimal clinically important difference for WOMAC scores. There was no significant difference in postoperative varus/valgus alignment between the two groups ( P = 0.092) Conclusion We found no clinically significant difference in any of the WOMAC domains in patients with preoperative varus deformity versus valgus deformity within the first year after TKR. These findings may allow surgeons to more appropriately counsel patients with osteoarthritis with valgus deformity that they can expect similar outcomes compared to patients with varus deformity.
INTERSUBJECTIVE BELIEF
Authors: Brown Vivienne 
Published: September 2017

ABSTRACTThis paper proposes a new model of shared belief amongst individual subjects based on a new approach to theorising individual subjects in social context. In this approach, which I term the intersubjective approach, individual subjects are modelled in terms of the standpoint of each of us, thereby incorporating the phenomenological standpoint of an individual subject's inclusion of herself within the plurality, ‘us’ (a class in the distributive sense). This provides resources for a new model of shared belief, including common belief, in terms of intersubjective belief, which is an individual subject's belief that ‘each of us has the same belief that p’. The paper argues that the intersubjective model of shared belief provides a non-reductive alternative to the standard interactive model of mutual belief and common belief, and so provides a non-individualistic framework for analysing shared belief in social contexts. As an illustration, the intersubjective model of common belief is applied to the Hi-Lo game; the solution is (High, High).
No nutritional benefits of egg cannibalism forColeomegilla maculata(Coleoptera: Coccinellidae) on a high-quality diet
Authors: Abdelwahab A.H. , Michaud J.P. , Bayoumy M.H. , Awadalla S.S. , El-Gendy M. 
Published: September 2017

AbstractEgg cannibalism serves various functions in the Coccinellidae. Here we examined the fitness consequences of egg cannibalism by neonates, fourth instar larvae, and prereproductive adults ofColeomegilla maculataDeGeer, with beetles fed a diet ofEphestia kuehniellaZeller eggs. Cannibalism of two eggs by neonates had no effect on development, and cannibalism of five eggs by fourth instars did not benefit any aspect of reproduction, but delayed pupation slightly. Cannibalism of eggs by pre-reproductive adults had no effect on reproductive success in any combination of reciprocal crosses of cannibals and non-cannibals. Females did not recognize, nor avoid consuming, their own clutches, and cannibalism propensity did not change following mating and onset of oviposition in either sex. These results contrast with those for more strictly aphidophagous species in which larvae gain developmental benefits, and females may recognize and avoid filial egg clusters while using cannibalism to interfere with conspecific females, whereas males reduce egg cannibalism after mating because they cannot recognize filial clusters. Egg cannibalism may confer developmental benefits toC. maculatawhen diet is suboptimal, as previously shown, but no such benefits were evident on the high-qualityE. kuehniellaegg diet. FemaleC. maculatado not require aphids to reproduce and distribute their eggs broadly in the environment, given that larvae can develop on pollen and non-aphid prey. Thus,C. maculatais not subject to the intraspecific competition that selects for cannibalism in more aphidophagous species, and also lacks many secondary adaptations associated with the behaviour.
Direct cost comparison of totally endoscopic versus open ear surgery
Authors: Patel N , Mohammadi A , Jufas N 
Published: September 2017

AbstractObjective:Totally endoscopic ear surgery is a relatively new method for managing chronic ear disease. This study aimed to test the null hypothesis that open and endoscopic approaches have similar direct costs for the management of attic cholesteatoma, from an Australian private hospital setting.Methods:A retrospective direct cost comparison of totally endoscopic ear surgery and traditional canal wall up mastoidectomy for the management of attic cholesteatoma in a private tertiary setting was undertaken. Indirect and future costs were excluded. A direct cost comparison of anaesthetic setup and resources, operative setup and resources, and surgical time was performed between the two techniques.Results:Totally endoscopic ear surgery has a mean direct cost reduction of AUD$2978.89 per operation from the hospital perspective, when compared to canal wall up mastoidectomy.Conclusion:Totally endoscopic ear surgery is more cost-effective, from an Australian private hospital perspective, than canal wall up mastoidectomy for attic cholesteatoma.
Maternal immune and affiliative biomarkers and sensitive parenting mediate the effects of chronic early trauma on child anxiety
Authors: Ulmer-Yaniv A. , Djalovski A. , Yirmiya K. , Halevi G. , Zagoory-Sharon O. , Feldman R. 
Published: September 2017

BackgroundChronic early trauma alters children's stress reactivity and increases the prevalence of anxiety disorders; yet the neuroendocrine and immune mechanisms underpinning this effect are not fully clear. Animal studies indicate that the mother's physiology and behavior mediate offspring stress in a system-specific manner, but few studies tested this external-regulatory maternal role in human children exposed to chronic stress.MethodsWe followed a unique cohort of children exposed to continuous wartime trauma (N= 177; exposed;N= 101, controls;N= 76). At 10 years, maternal and child's salivary immunoglobulin A (s-IgA) and oxytocin (OT), biomarkers of the immune and affiliation systems, were assayed, maternal and child relational behaviors observed, mother and child underwent psychiatric diagnosis, and child anxiety symptoms assessed.ResultsWar-exposed mothers had higher s-IgA, lower OT, more anxiety symptoms, and their parenting was characterized by reduced sensitivity. Exposed children showed higher s-IgA, more anxiety disorders and post traumatic stress disorder, and more anxiety symptoms. Path analysis model defined three pathways by which maternal physiology and behavior impacted child anxiety; (a) increasing maternal s-IgA, which led to increased child s-IgA, augmenting child anxiety; (b) reducing maternal OT, which linked with diminished child OT and social repertoire; and (c) increasing maternal anxiety, which directly impacted child anxiety.ConclusionsOur findings, the first to measure immune and affiliation biomarkers in mothers and children, detail their unique and joint effects on children's anxiety in response to stress; highlight the relations between chronic stress, immune activation, and anxiety in children; and describe how processes of biobehavioral synchrony shape children's long-term adaptation.
Transcriptomics ofnine-cis-epoxycarotenoid dioxygenase 6induction in imbibed seeds reveals feedback mechanisms and long non-coding RNAs
Authors: Sall Khadidiatou , Hendrix David , Sekine Taira , Katsuragawa Yoshihiko , Koyari Ryosuke , Nonogaki Hiroyuki 
Published: September 2017

AbstractInductionof nine-cis-epoxycarotenoid dioxygenase 6(NCED6), an abscisic acid (ABA) biosynthesis gene, alone is sufficient to suspend germination in testa-ruptured seeds, which are at the final step of germination. Molecular consequences ofNCED6induction in imbibed seeds were investigated by RNA sequencing. The analysis identified many unknown and uncharacterized genes that were up-regulated byNCED6induction, in addition to the major regulators of ABA signalling. Interestingly, otherNCEDs were up-regulated byNCED6induction, suggesting that the major rate-limiting enzymes in the ABA biosynthesis pathway are subject to positive-feedback regulation.ZEAXANTHIN EPOXIDASEandABSCISIC ALDEHYDE OXIDASE3, which function upstream and downstream ofNCED, were also up-regulated in seeds byNCED6induction, which suggests that the distinct layers of positive feedback loops are coordinately operating in theNCED6-induced seeds.SOMNUS(SOM), which was also up-regulated byNCED6induction, was the major mediator of enhanced ABA signalling inNCED6-induced seeds.SOMexerted negative effects on GA biosynthesis, which also contributes to a high ABA–GA ratio and reinforces the suppressive state of germination. Besides these coding genes, long intergenic non-coding RNAs (lincRNAs) were also up-regulated uponNCED6induction (termedN6LINCRs). Conditional expression ofN6LINCR1altered gene expression profiles in seeds. Twenty-six genes were up-regulated and 66 genes were down-regulated by the induction ofN6LINCR1. These results suggest that some ofN6LINCRshave a regulatory role in gene expression in seeds, which potentially contributes to the regulation of germination by ABA.
Problematic internet use in gamblers: impact on clinical and cognitive measures
Authors: Chamberlain Samuel R. , Redden Sarah A. , Leppink Eric , Grant Jon E. 
Published: September 2017

ObjectiveGambling is a commonplace phenomenon, existing along a continuum from occasional gambling to functionally impairing gambling disorder. The internet may act as a conduit for some gambling behaviors. The impact of problematic internet use on clinical and cognitive features relevant to gambling has received little research attention.MethodsA total of 206 adults aged 18–30 years who gamble at least five times per year were recruited from the general community and undertook detailed clinical and cognitive assessments. Problematic internet use was defined using a total score of 5 or more on Young’s Diagnostic Questionnaire (YDQ). Linear regression was employed to evaluate the relative contribution of addictive-related, impulsive-related, and compulsive-related measures in predicting YDQ total scores in gamblers.ResultsGamblers with problematic internet use (18% of the sample) reported lower quality of life, lower self-esteem, elevated rates of intermittent explosive disorder, gambling disorder symptoms, attention deficit hyperactivity disorder (ADHD) symptoms, antisocial personality disorder, and posttraumatic stress disorder (PTSD), as well as relative deficits in decision making and spatial working memory. In linear regression, the extent of problematic internet use was most significantly associated with increased gambling disorder symptoms and increased ADHD symptoms.ConclusionsProblematic internet use in gamblers is associated with worse quality of life, more problem/pathological gambling symptoms, more psychiatric morbidities, and select cognitive impairment. Refinement of the definition of problematic internet use and exploration of its clinical and cognitive associations are likely to be highly relevant to the treatment of problematic gambling.
Uncontrolled angiogenic precursor expansion causes coronary artery anomalies in mice lacking Pofut1
Authors: Wang Yidong , Wu Bingruo , Lu Pengfei , Zhang Donghong , Wu Brian , Varshney Shweta , del Monte-Nieto Gonzalo , Zhuang Zhenwu , Charafeddine Rabab , Kramer Adam H. , Sibinga Nicolas E. , Frangogiannis Nikolaos G. , Kitsis Richard N. , Adams Ralf H. , Alitalo Kari , Sharp David J. , Harvey Richard P. , Stanley Pamela , Zhou Bin 
Published: September 2017

AbstractCoronary artery anomalies may cause life-threatening cardiac complications; however, developmental mechanisms underpinning coronary artery formation remain ill-defined. Here we identify an angiogenic cell population for coronary artery formation in mice. Regulated by a DLL4/NOTCH1/VEGFA/VEGFR2 signaling axis, these angiogenic cells generate mature coronary arteries. The NOTCH modulator POFUT1 critically regulates this signaling axis. POFUT1 inactivation disrupts signaling events and results in excessive angiogenic cell proliferation and plexus formation, leading to anomalous coronary arteries, myocardial infarction and heart failure. Simultaneous VEGFR2 inactivation fully rescues these defects. These findings show that dysregulated angiogenic precursors link coronary anomalies to ischemic heart disease.
MANF regulates hypothalamic control of food intake and body weight
Authors: Yang Su , Yang Huiming , Chang Renbao , Yin Peng , Yang Yang , Yang Weili , Huang Shanshan , Gaertig Marta A. , Li Shihua , Li Xiao-Jiang 
Published: September 2017

AbstractThe hypothalamus has a vital role in controlling food intake and energy homeostasis; its activity is modulated by neuropeptides and endocrine factors. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a neurotrophic factor that is also localized in the endoplasmic reticulum (ER) in neurons. Here we show that MANF is highly enriched in distinct nuclei of the mouse hypothalamus, and that MANF expression in the hypothalamus is upregulated in response to fasting. Increasing or decreasing hypothalamic MANF protein levels causes hyperphagia or hypophagia, respectively. Moreover, MANF triggers hypothalamic insulin resistance by enhancing the ER localization and activity of PIP4k2b, a kinase known to regulate insulin signaling. Our findings indicate that MANF influences food intake and body weight by modulating hypothalamic insulin signaling.
Expression of brown-midrib in a spontaneous sorghum mutant is linked to a 5′-UTR deletion in lignin biosynthesis gene SbCAD2
Authors: Li Huang , Huang Yinghua 
Published: September 2017

AbstractBrown midrib (bmr) mutants in sorghum (Sorghum bicolor (L.) Moench) and several other C4 grasses are associated with reduced lignin concentration, altered lignin composition and improved cell wall digestibility, which are desirable properties in biomass development for the emerging lignocellulosic biofuel industry. Studying bmr mutants has considerably expanded our understanding of the molecular basis underlying lignin biosynthesis and perturbation in grasses. In this study, we performed quantitative trait locus (QTL) analysis, identified and cloned a novel cinnamyl alcohol dehydrogenase allele (SbCAD2) that has an 8-bp deletion in its 5′-untranslated region (UTR), conferring the spontaneous brown midrib trait and lignin reduction in the sorghum germplasm line PI 595743. Complementation test and gene expression analysis revealed that this non-coding region alteration is associated with the significantly reduced expression of the SbCAD2 in PI 595743 throughout its growth stages. Moreover, a promoter-GUS fusion study with transgenic Arabidopsis thaliana plants found that SbCAD2 promoter is functionally conserved, driving a specific expression pattern in lignifying vascular tissues. Taken together, our results revealed the genetic basis of bmr occurrence in this spontaneous sorghum mutant and suggested the regulatory region of the SbCAD2 can be a target site for optimizing lignin modification in sorghum and other bioenergy crops.
Analysis of VSV pseudotype virus infection mediated by rubella virus envelope proteins
Authors: Sakata Masafumi , Tani Hideki , Anraku Masaki , Kataoka Michiyo , Nagata Noriyo , Seki Fumio , Tahara Maino , Otsuki Noriyuki , Okamoto Kiyoko , Takeda Makoto , Mori Yoshio 
Published: September 2017

AbstractRubella virus (RV) generally causes a systemic infection in humans. Viral cell tropism is a key determinant of viral pathogenesis, but the tropism of RV is currently poorly understood. We analyzed various human cell lines and determined that RV only establishes an infection efficiently in particular non-immune cell lines. To establish an infection the host cells must be susceptible and permissible. To assess the susceptibility of individual cell lines, we generated a pseudotype vesicular stomatitis virus bearing RV envelope proteins (VSV-RV/CE2E1). VSV-RV/CE2E1 entered cells in an RV envelope protein-dependent manner, and thus the infection was neutralized completely by an RV-specific antibody. The infection was Ca2+-dependent and inhibited by endosomal acidification inhibitors, further confirming the dependency on RV envelope proteins for the VSV-RV/CE2E1 infection. Human non-immune cell lines were mostly susceptible to VSV-RV/CE2E1, while immune cell lines were much less susceptible than non-immune cell lines. However, susceptibility of immune cells to VSV-RV/CE2E1 was increased upon stimulation of these cells. Our data therefore suggest that immune cells are generally less susceptible to RV infection than non-immune cells, but the susceptibility of immune cells is enhanced upon stimulation.