bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction of (2‐CF3)Phenyl Group via Nickel‐catalyzed C–Cl Bond Activation and Arylation
Authors: Peng Zheng , Sun Hongjian , Du Aiqin , Li Xiaoyan 
Published: February 2015

Abstract A simple and mild catalytic arylation via C–Cl bond activation is described. The phenyl group containing a 2‐trifluoromethyl group was introduced into the aromatic imine molecules through C,C‐coupling reaction between chloroarenes and the organozinc reagent, bis(2‐(trifluoromethyl)phenyl)zinc, with tetrakis(trimethylphosphine)nickel(0) complex as an effective catalyst. Under catalytic conditions chlorinated benzalimines were quantitatively converted into the expected benzalimines with trifluoromethyl group(s).
Determining the influence of Itaipu Lake on thermal conditions for soybean development in adjacent lands
Authors: Wagner-Riddle C. , Werner S. S. , Caramori P. , Ricce W. S. , Nitsche P. , von Bertoldi P. , de Souza E. F. 
Published: February 2015

Abstract
Previous numerical simulations have suggested that the area adjacent to Itaipu Lake in Southern Brazil is significantly affecting the local thermal regime through development of a lake breeze. This has led to concerns that soybean growth and development, and consequently yield, has been affected by the creation of the artificial lake in this important agricultural region, but a systematic climatological study of the thermal effects of Itaipu Lake has not been conducted. The objectives of this study were to assess the spatial pattern of minimum and maximum air temperatures in a 10-km-wide area adjacent to Itaipu Lake as affected by distance from the water. Measurements were conducted over 3 years in seven transects along the shore of Itaipu Lake, with five weather stations placed in each transect. Phenological observations in soybean fields surrounding the weather stations were also conducted. Generalized additive models for location, scale, and shape (GAMLSS) analysis indicated no difference in the temperature time series as distance from water increased. Semivariograms showed that the random components in the air temperature were predominant and that there was no spatial structure to the signal. Wind direction measured over the three growing seasons demonstrated that, on average, the development of a lake breeze is limited to a few locations and a few hours of the day, supporting the temporal and spatial analysis. Phenological observations did not show differences in the timing of critical soybean stages. We suggest that the concerns that soybean development is potentially affected by the presence of Itaipu Lake are not supported by the thermal environment observed.
Psychological Impact of Predictive Genetic Testing in VCP Inclusion Body Myopathy, Paget Disease of Bone and Frontotemporal Dementia
Authors: Surampalli Abhilasha , Khare Manaswitha , Kubrussi Georgette , Wencel Marie , Tanaja Jasmin , Donkervoort Sandra , Osann Kathryn , Simon Mariella , Wallace Douglas , Smith Charles , M.McInerney‐Leo Aideen , Kimonis Virginia 
Published: February 2015

AbstractInclusion Body Myopathy associated with Paget's disease of bone and Fronto‐temporal Dementia, also known as multisystem proteinopathy is an autosomal dominant, late onset neurodegenerative disorder caused by mutations in Valosin containing protein (VCP) gene. This study aimed to assess uptake and decision making for predictive genetic testing and the impact on psychological well‐being. Individuals who had participated in the gene discovery study with a 50 % a priori risk of inheriting VCP disease were sent a letter of invitation offering genetic counseling and testing and were also invited to participate in this psychosocial study. A total of 102 individuals received an invitation and 33 individuals participated in genetic counseling and testing (32.3 %) with 29 completing baseline questionnaires. Twenty completed the follow‐up post‐test Hospital Anxiety and Depression Scale questionnaire including 13 of the 18 who had tested positive. Mean risk perception at baseline was 50.1 %. Reasons for testing included planning for the future, relieving uncertainty, informing children and satisfying curiosity. At baseline, one quarter of the participants had high levels of anxiety. However, scores were normal one year following testing. In this small cohort, one third of individuals at 50 % risk chose pre‐symptomatic testing. Although one quarter of those choosing testing had high anxiety at baseline, this was not evident at follow‐up.
Ethnic Variations in Immigrant Poverty Exit and Female Employment: The Missing Link
Authors: Kaida Lisa 
Published: February 2015

AbstractDespite widespread interest in poverty among recent immigrants and female immigrant employment, research on the link between the two is limited. This study evaluates the effect of recently arrived immigrant women’s employment on the exit from family poverty and considers the implications for ethnic differences in poverty exit. It uses the bivariate probit model and the Fairlie decomposition technique to analyze data from the Longitudinal Survey of Immigrants to Canada (LSIC), a nationally representative survey of immigrants arriving in Canada, 2000–2001. Results show that the employment of recently arrived immigrant women makes a notable contribution to lifting families out of poverty. Moreover, the wide ethnic variations in the probability of exit from poverty between European and non-European groups are partially explained by the lower employment rates among non-European women. The results suggest that the equal earner/female breadwinner model applies to low-income recent immigrant families in general, but the male breadwinner model explains the low probability of poverty exit among select non-European groups whose female employment rates are notably low.
Global efforts for effective training in fistula surgery
Authors: Elneil Sohier 
Published: February 2015

AbstractObstetric fistulas continue to be a problem in low‐ and middle‐income nations, affecting women of childbearing age during pregnancy and labor and resulting in debilitating urinary and/or fecal incontinence. Historically, this predicament also affected women in high‐income nations until the middle of the last century. This is not a “new world” crisis therefore, but simply one of economic and health development. In the last two decades, new global initiatives have been instituted to improve training and education in preventative and curative fistula treatment by developing a unified and competency‐based learning tool by surgeons in the field in partnership with FIGO and its global partners. This modern approach to the management of a devastating condition can only serve to achieve the WHO objective of health security for women throughout their life span.
Ecological consequences of the Guadalupian extinction and its role in the brachiopod-mollusk transition
Authors: Clapham Matthew E. 
Published: February 2015

AbstractThe Guadalupian (middle Permian) extinction may have triggered substantial ecological restructuring in level-bottom communities, such as turnover in dominant brachiopod genera or a shift from abundant brachiopods to mollusks, despite comparatively minor taxonomic losses. However, ecological changes in relative abundance have been inferred from limited data; as a result, constraints on important shifts like the brachiopod-mollusk transition are imprecise. Here, I reevaluate the magnitude of ecological shifts during the Guadalupian–Lopingian (G-L) interval by supplementing previous census counts of silicified assemblages with counts from non-silicified assemblages and global occurrence data, both sourced from the Paleobiology Database. Brachiopod occurrences are consistent with more pronounced faunal composition changes from the Guadalupian to Lopingian than among stages within those intervals, but only in Iran and South China, and not in Pakistan or a Tethys-wide data set. In Iran and South China, Bray-Curtis dissimilarity values comparing occurrence frequencies between adjacent stages were elevated across the G-L transition, although other intervals exhibited similarly large shifts. However, genus occurrence frequencies were less strongly correlated or were anti-correlated across the G-L transition, suggesting moderate faunal turnover among dominant brachiopod genera. In contrast to previous inferences from silicified faunas, abundances of brachiopods, bivalves, and gastropods remained consistent from the Guadalupian to Lopingian in non-silicified local counts and global occurrences, implying that the brachiopod-mollusk shift did not occur until the end-Permian extinction. Ecological and taxonomic consequences were both minor in level-bottom settings, suggesting that severe environmental perturbations may not be necessary to explain biotic changes during the Guadalupian-Lopingian transition.
Preservation is predictable: quantifying the effect of taphonomic biases on ecological disparity in birds
Authors: Mitchell Jonathan S. 
Published: February 2015

AbstractEvolutionary inferences from fossil data often require accurately reconstructing differences in richness and morphological disparity between fossil sites across space and time. Biases such as sampling and rock availability are commonly accounted for in large-scale studies; however, preservation bias is usually dealt with only in smaller, more focused studies. Birds represent a diverse, but taphonomically fragile, group commonly used to infer environmental conditions in recent (Pleistocene and later) fossil assemblages, and their relative scarcity in the fossil record has led to controversy over the timing of their radiation. Here, I use simulations to show how even weak taphonomic biases can distort estimates of richness, and render variance sensitive to sample size. I then apply an ecology-based filtering model to recent bird assemblages to quantify the distortion induced by taphonomy. Certain deposit types, such as caves, show less evidence of taphonomic distortion than others, such as fluvial and lacustrine deposits. Archaeological middens unsurprisingly show some of the strongest evidence for taphonomic bias, and they should be avoided when reconstructing Pleistocene and early Holocene environments. Further, these results support previously suggested methods for detecting fossil assemblages that are relatively faithfully preserved (e.g., presence of difficult-to-preserve taxa), and I use these results to recommend that future large-scale studies include facies diversity along with metrics such as rock volume, or compare only sites with similar taphonomic histories.
Music Physicianers: Blues Lyric Form and the Patent Medicine Show
Authors: SANDLER MATT 
Published: February 2015

Patent medicine shows became popular in the United States around the turn of the twentieth century by selling their products alongside free musical and theatrical entertainments. The “doctors” promised a range of cures, but usually mixed their remedies with alcohol or narcotics – using the promise of health to evade religious authorities and law enforcement, even in dry counties. Many talented black performers toured with medicine shows, including a number of artists later associated with the blues. I argue that the medicine show had a decisive impact on the blues by providing not simply training in performance, but also an impetus for the notorious suggestiveness of its lyric code. The blues borrows from the medicine show its lawless appeal to ailments uncategorized and ignored by socially sanctioned experts.
An analytical framework for optimizing variant discovery from personal genomes
Authors: Highnam Gareth , Wang Jason J. , Kusler Dean , Zook Justin , Vijayan Vinaya , Leibovich Nir , Mittelman David 
Published: February 2015

AbstractThe standardization and performance testing of analysis tools is a prerequisite to widespread adoption of genome-wide sequencing, particularly in the clinic. However, performance testing is currently complicated by the paucity of standards and comparison metrics, as well as by the heterogeneity in sequencing platforms, applications and protocols. Here we present the genome comparison and analytic testing (GCAT) platform to facilitate development of performance metrics and comparisons of analysis tools across these metrics. Performance is reported through interactive visualizations of benchmark and performance testing data, with support for data slicing and filtering. The platform is freely accessible at http://www.bioplanet.com/gcat.
A Dual-Intein Autoprocessing Domain that Directs Synchronized Protein Co-Expression in Both Prokaryotes and Eukaryotes
Authors: Zhang Bei , Rapolu Madhusudhan , Liang Zhibin , Han Zhenlin , Williams Philip G. , Su Wei Wen 
Published: February 2015

AbstractBeing able to coordinate co-expression of multiple proteins is necessary for a variety of important applications such as assembly of protein complexes, trait stacking and metabolic engineering. Currently only few options are available for multiple recombinant protein co-expression and most of them are not applicable to both prokaryotic and eukaryotic hosts. Here, we report a new polyprotein vector system that is based on a pair of self-excising mini-inteins fused in tandem, termed the dual-intein (DI) domain, to achieve synchronized co-expression of multiple proteins. The DI domain comprises an Ssp DnaE mini-intein N159A mutant and an Ssp DnaB mini-intein C1A mutant connected in tandem by a peptide linker to mediate efficient release of the flanking proteins via autocatalytic cleavage. Essentially complete release of constituent proteins, GFP and RFP (mCherry), from a polyprotein precursor, in bacterial, mammalian and plant hosts was demonstrated. In addition, successful co-expression of GFP with chloramphenicol acetyltransferase and thioredoxin with RFP, respectively, further substantiates the general applicability of the DI polyprotein system. Collectively, our results demonstrate the DI-based polyprotein technology as a highly valuable addition to the molecular toolbox for multi-protein co-expression which finds vast applications in biotechnology, biosciences and biomedicine.
Identification of Two Structural Elements Important for Ribosome-Dependent GTPase Activity of Elongation Factor 4 (EF4/LepA)
Authors: De Laurentiis Evelina Ines , Wieden Hans-Joachim 
Published: February 2015

AbstractThe bacterial translational GTPase EF4/LepA is structurally similar to the canonical elongation factor EF-G. While sharing core structural features with other translational GTPases, the function of EF4 remains unknown. Recent structural data locates the unique C-terminal domain (CTD) of EF4 in proximity to the ribosomal peptidyl transferase center (PTC). To investigate the functional role of EF4's CTD we have constructed three C-terminal truncation variants. These variants are fully functional with respect to binding mant-GTP and mant-GDP as determined by rapid kinetics, as well as their intrinsic multiple turnover GTPase activity. Furthermore, they are able to form stable complexes with the 70S ribosome and 50S/30S ribosomal subunits. However, successive removal of the C-terminus impairs ribosome-dependent multiple turnover GTPase activity of EF4, which for the full-length protein is very similar to EF-G. Our findings suggest that the last 44 C-terminal amino acids of EF4 form a sub-domain within the C-terminal domain that is important for GTP-dependent function on the ribosome. Additionally, we show that efficient nucleotide hydrolysis by EF4 on the ribosome depends on a conserved histidine (His 81), similar to EF-G and EF-Tu.
An ensemble-averaged, cell density-based digital model of zebrafish embryo development derived from light-sheet microscopy data with single-cell resolution
Authors: Kobitski Andrei Y. , Otte Jens C. , Takamiya Masanari , Schäfer Benjamin , Mertes Jonas , Stegmaier Johannes , Rastegar Sepand , Rindone Francesca , Hartmann Volker , Stotzka Rainer , García Ariel , van Wezel Jos , Mikut Ralf , Strähle Uwe , Nienhaus G. Ulrich 
Published: February 2015

AbstractA new era in developmental biology has been ushered in by recent advances in the quantitative imaging of all-cell morphogenesis in living organisms. Here we have developed a light-sheet fluorescence microscopy-based framework with single-cell resolution for identification and characterization of subtle phenotypical changes of millimeter-sized organisms. Such a comparative study requires analyses of entire ensembles to be able to distinguish sample-to-sample variations from definitive phenotypical changes. We present a kinetic digital model of zebrafish embryos up to 16 h of development. The model is based on the precise overlay and averaging of data taken on multiple individuals and describes the cell density and its migration direction at every point in time. Quantitative metrics for multi-sample comparative studies have been introduced to analyze developmental variations within the ensemble. The digital model may serve as a canvas on which the behavior of cellular subpopulations can be studied. As an example, we have investigated cellular rearrangements during germ layer formation at the onset of gastrulation. A comparison of the one-eyed pinhead (oep) mutant with the digital model of the wild-type embryo reveals its abnormal development at the onset of gastrulation, many hours before changes are obvious to the eye.
Pharmacological recruitment of aldehyde dehydrogenase 3A1 (ALDH3A1) to assist ALDH2 in acetaldehyde and ethanol metabolism in vivo
Authors: Chen Che-Hong , Cruz Leslie A. , Mochly-Rosen Daria 
Published: February 2015

Significance
About 560 million East Asians have an impaired ability to eliminate acetaldehyde because of a point mutation in an enzyme called aldehyde dehydrogenase 2 (ALDH2). Humans with this mutation have ∼20-fold higher blood acetaldehyde levels than those with normal enzyme activity after consuming one to two units of alcoholic beverages. Because acetaldehyde is a potent carcinogen and causes behavioral impairment, its accumulation is a health risk. We identified a pharmacologic agent that recruits ALDH3A1, a closely related enzyme, to compensate for a loss of ability of ALDH2 to metabolize acetaldehyde. Pharmacologic agents that alter substrate specificity of an enzyme have not yet been described and may have wide clinical application in treating patients with impaired ability to detoxify toxic substances.
Large number of rebounding/founder HIV variants emerge from multifocal infection in lymphatic tissues after treatment interruption
Authors: Rothenberger Meghan K. , Keele Brandon F. , Wietgrefe Stephen W. , Fletcher Courtney V. , Beilman Gregory J. , Chipman Jeffrey G. , Khoruts Alexander , Estes Jacob D. , Anderson Jodi , Callisto Samuel P. , Schmidt Thomas E. , Thorkelson Ann , Reilly Cavan , Perkey Katherine , Reimann Thomas G. , Utay Netanya S. , Nganou Makamdop Krystelle , Stevenson Mario , Douek Daniel C. , Haase Ashley T. , Schacker Timothy W. 
Published: February 2015

Significance
Antiretroviral therapy (ART) effectively suppresses HIV replication; however, treatment cannot be stopped, because latently infected CD4+ T cells will rekindle infection. As one estimate of the size of the pool of latently infected cells that must be purged for cure, we asked whether recrudescent infection is the result of reactivation from one or a larger number latently infected cells. We briefly stopped ART in fully suppressed patients to see how widespread new infections were in the lymphoid tissues (LTs) and how diverse rebounding/founder viruses were in peripheral blood. Recrudescent infection was detectable in multiple different LTs, and the population was genetically diverse, consistent with reactivation from a larger number of cells. These findings underscore the challenges facing strategies to eradicate HIV infection.
Cross-language differences in the brain network subserving intelligible speech
Authors: Ge Jianqiao , Peng Gang , Lyu Bingjiang , Wang Yi , Zhuo Yan , Niu Zhendong , Tan Li Hai , Leff Alexander P. , Gao Jia-Hong 
Published: February 2015

Significance
Language processing is generally left hemisphere dominant. However, whether the interactions among the typical left hemispheric language regions differ across different languages is largely unknown. An ideal method to address this question is modeling cortical interactions across language groups, but this is usually constrained by the model space with the prior hypothesis due to massive computation demands. With cloud-computing, we used functional MRI dynamic causal modeling analysis to compare more than 4,000 models of cortical dynamics among critical language regions in the temporal and frontal cortex, established the bias-free information flow maps that were shared or specific for processing intelligible speech in Chinese and English, and revealed the neural dynamics between the left and right hemispheres in Chinese speech comprehension.
Network compensation of cyclic GMP-dependent protein kinase II knockout in the hippocampus by Ca
2+
-permeable AMPA receptors
Authors: Kim Seonil , Titcombe Roseann F. , Zhang Hong , Khatri Latika , Girma Hiwot K. , Hofmann Franz , Arancio Ottavio , Ziff Edward B. 
Published: February 2015

Significance
Deletion of genes in organisms does not always give rise to phenotypes because of the existence of compensation, even though phenotypes may be found when gene activity is blocked acutely. The cGMP-dependent kinase II knockout is a typical example of this apparent paradox. The knockout shows no evident impairment of LTP, whereas acute inhibition of kinase activity significantly decreases it. This paper describes a previously unidentified form of network-based compensation for cGMP-dependent kinase II gene knockout that is not dependent on expression of duplicate or paralogous genes. Furthermore, the compensation described here is mediated by a mechanism similar to that used by activity-dependent homeostatic synaptic plasticity, suggesting that neurons in complex brains may overcome an unexpected genetic lesion by using existing homeostatic mechanisms.
Differential fates of biomolecules delivered to target cells via extracellular vesicles
Authors: Kanada Masamitsu , Bachmann Michael H. , Hardy Jonathan W. , Frimannson Daniel Omar , Bronsart Laura , Wang Andrew , Sylvester Matthew D. , Schmidt Tobi L. , Kaspar Roger L. , Butte Manish J. , Matin A. C. , Contag Christopher H. 
Published: February 2015

Significance
Extracellular vesicle (EV)-mediated transfer of macromolecules may play a key role in cellular communication and may have utility in directed molecular therapies. In addition, the EV packaged biomolecules in serum may have potential for diagnosing cancer and determining its likelihood of metastasis. EVs are heterogeneous and there are many outstanding questions associated with biogenesis, uptake, and the fate of transferred molecules in recipient cells. In fact, the function, characterization, and even the nomenclature of EVs are being refined. Here we aimed to improve the functional characterization of EVs, and observed that only microvesicles (MVs), but not exosomes, can functionally transfer loaded reporter molecules to recipient cells, largely by delivering plasmid DNA. Our data show that exosomes and MVs are structurally and functionally distinct.