bluuebunny/crossref_metadata_2025 huggingface dataset:
Hollow PtPdRh Nanocubes with Enhanced Catalytic Activities for In Vivo Clearance of Radiation‐Induced ROS via Surface‐Mediated Bond Breaking
Authors: Wang Jun‐Ying , Mu Xiaoyu , Li Yonghui , Xu Fujuan , Long Wei , Yang Jiang , Bian Peixian , Chen Junchi , Ouyang Lufei , Liu Haile , Jing Yaqi , Wang Jingya , Liu Lingfang , Dai Haitao , Sun Yuanming , Liu Changlong , Zhang Xiao‐Dong
Published: February 2018

Catalytic nanomaterials can be used extrinsically to combat diseases associated with a surplus of reactive oxygen species (ROS). Rational design of surface morphologies and appropriate doping can substantially improve the catalytic performances. In this work, a class of hollow polyvinyl pyrrolidone‐protected PtPdRh nanocubes with enhanced catalytic activities for in vivo free radical scavenging is proposed. Compared with Pt and PtPd counterparts, ternary PtPdRh nanocubes show remarkable catalytic properties of decomposing H2O2 via enhanced oxygen reduction reactions. Density functional theory calculation indicates that the bond of superoxide anions breaks for the energetically favorable status of oxygen atoms on the surface of PtPdRh. Viability of cells and survival rate of animal models under exposure of high‐energy γ radiation are considerably enhanced by 94% and 50% respectively after treatment of PtPdRh nanocubes. The mechanistic investigations on superoxide dismutase (SOD) activity, malondialdehyde amount, and DNA damage repair demonstrate that hollow PtPdRh nanocubes act as catalase, peroxidase, and SOD analogs to efficiently scavenge ROS.
Petri net modeling and analysis of an iPad manufacturing system
Authors: Shen Rong‐Kuan , Chiou Gwo‐Jen , Yang Cheng‐Ying , Shen Victor R.L. , Chen Yu‐Chia
Published: February 2018

The ever increasing sales of Apple's iPad have created a tablet computer craze, attracting various manufacturers to invest and conduct research in this sector. Meanwhile, the production cost is crucial to being considered in the craze. To lower the cost, manufacturers are striving to develop reasonable and complete manufacturing processes. We have herewith proposed a Petri net model to describe the system structure and to label out the simulated operation messages or dynamic decision‐making behaviors. The key minimal cost path is finally found so as to manifest the optimal decision‐making on the production flow. Finally, the software tool, PIPE‐2, is used to verify the algorithm of finding the minimal cost path. Thus, the experimental results successfully demonstrate the feasibility of the proposed approach.
Relative Bias and Precision of Age Estimates among Calcified Structures of Spotted Gar, Shortnose Gar, and Longnose Gar
Authors: King Sarah M. , David Solomon R. , Stein Jeffrey A.
Published: February 2018

Recreational angling for gars (family Lepisosteidae) has become more popular in recent years; however, the fundamental understanding of their population dynamics needed for effective management and conservation is lacking. Age data are essential for describing population dynamic rate functions, but few studies have addressed the selection of ideal calcified structures for estimating age in gars. We collected Spotted Gars Lepisosteus oculatus, Shortnose Gars L. platostomus, and Longnose Gars L. osseus from 12 Illinois water bodies to assess the relative bias and precision of age estimates derived from branchiostegal rays, pectoral fin rays, cleithra, and sagittal otoliths. Age assignments differed among these calcified structures for all three species. Branchiostegal rays underestimated the age of young fish and overestimated the age of old fish relative to all other structures. Pectoral fin rays consistently underestimated age relative to other structures and produced the lowest mean and maximum age estimates. Although there was low relative bias between readers for all structures, age assignments showed greater variability between readers for old age‐classes when age estimates were derived from cleithra and otoliths. Between‐reader precision was highest using pectoral fin rays, whereas cleithra and otoliths generated lower coefficients of variation and percent agreement values. These findings reveal a need to improve or modify structure processing methods to increase readability when cleithra and otoliths are used for age estimation. Given these results, future validation studies should target branchiostegal rays and pectoral fin rays to determine the most accurate calcified structure for aging gars.
Comparison of Two Biometric Methods for Nonlethal Sex Determination of Alligator Gars
Authors: McDonald Dusty L. , Schlechte J. Warren , Daugherty Daniel J.
Published: February 2018

McDonald et al. () proposed a morphometry‐based method for nonlethal sex prediction of the Alligator Gar Atractosteus spatula. Their method correctly predicted the sex of 93% of the males and 72% of the females tested, but failed to predict the sex of 21% of the fish. The authors noted that the method was primarily developed using immature fish from a single Texas population and recommended further validation and refinement using fish of diverse sizes from a broad range of systems. We tested the McDonald et al. () method using 149 fish (standard length, 707–1,920 mm) collected from seven Texas populations. Sex prediction based on the McDonald et al. () method improved for both sexes (98% of males and 86% of females); however, sex still could not be predicted for 29% of the fish. As a result, we explored the use of a cross‐validated, discriminant function analysis (DFA) using the morphometric ratios developed by McDonald et al. () to improve our ability to predict the sex of sampled fish. The DFA facilitated probability‐based predictions of all fish sampled and had an overall accuracy of 84% for males and 89% for females. Logistic regression based on the success of the DFA suggested that fish >1,100 mm SL are easier to identify using the morphometric ratios (>90% accuracy), likely because changes in body shape are associated with sexual maturity. In addition to predicting the sex of all of the fish sampled, the DFA approach facilitated calculation of the probability of correct discrimination for each fish. Due to these advantages, along with its comparable accuracy, we recommend the use of the DFA approach over the method proposed by McDonald et al. () for predicting the sex of Alligator Gars.
Circadian processes in the RNA life cycle
Authors: Torres Manon , Becquet Denis , Franc Jean‐Louis , François‐Bellan Anne‐Marie
Published: February 2018

The circadian clock drives daily rhythms of multiple physiological processes, allowing organisms to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of at least 30% of expressed genes. While the ability for the endogenous timekeeping system to generate a 24‐hr cycle is a cell‐autonomous mechanism based on negative autoregulatory feedback loops of transcription and translation involving core‐clock genes and their protein products, it is now increasingly evident that additional mechanisms also govern the circadian oscillations of clock‐controlled genes. Such mechanisms can take place post‐transcriptionally during the course of the RNA life cycle. It has been shown that many steps during RNA processing are regulated in a circadian manner, thus contributing to circadian gene expression. These steps include mRNA capping, alternative splicing, changes in splicing efficiency, and changes in RNA stability controlled by the tail length of polyadenylation or the use of alternative polyadenylation sites. RNA transport can also follow a circadian pattern, with a circadian nuclear retention driven by rhythmic expression within the nucleus of particular bodies (the paraspeckles) and circadian export to the cytoplasm driven by rhythmic proteins acting like cargo. Finally, RNA degradation may also follow a circadian pattern through the rhythmic involvement of miRNAs. In this review, we summarize the current knowledge of the post‐transcriptional circadian mechanisms known to play a prominent role in shaping circadian gene expression in mammals.

This article is categorized under:

RNA Processing > Splicing Regulation/Alternative Splicing

RNA Processing > RNA Editing and Modification

RNA Export and Localization > Nuclear Export/Import
Wavefronts and shocks in the vicinity of sonic lines
Authors: Núñez Manuel
Published: February 2018

Sonic points in an equilibrium fluid are those for which the speed of sound equals the flow velocity. We study how high frequency waves evolve in the presence of sonic points. It is shown that their behavior depends in an essential way on the original direction of the wave normal, and the effects of sonic points extend far beyond their immediate vicinity. The transport equation along rays of perturbations of the original equilibrium is also detailed, obtaining conditions for their evolution into shocks.
Depression Induced by Total Mastectomy, Breast Conserving Surgery and Breast Reconstruction: A Systematic Review and Meta‐analysis
Authors: Zhang Chengjiao , Hu Guangfu , Biskup Ewelina , Qiu Xiaochun , Zhang Hongwei , Zhang Haiyin
Published: February 2018

Background

To carry out a systematic review and meta‐analysis of the literature to determine whether different type of surgery induces different depression occurrence in female breast cancer at mean time more than 1‐year term postoperatively.

Methods

A systematic literature search of PubMed, Web of Science, EMBASE, OvidSP, EBSCO and PsycARTICLES was conducted. Observational clinical studies that compared the depression incidence in different surgery groups and presented empirical findings were selected.

Results

Sixteen studies met the inclusion criteria, including 5, 4, 2 and 5 studies compared depression between total mastectomy (TM) and breast conserving therapy (BCS), TM and breast reconstruction (BR), BCS and BR, or among all three groups (TM, BCS and BR), respectively. Only 1 of 5 studies, which subjected to multivariate analysis of depression in female breast cancer, reported a statistically significant effect of type of surgery on depression occurrence. Our meta‐analysis showed no significant differences among the three types of surgery, with BCS patients versus TM patients (relative risk [RR] = 0.89, 95% confidence interval [CI] 0.78–1.01; P = 0.06), BR patients versus TM patients (RR = 0.87, 95% CI 0.71–1.06; P = 0.16) and BCS patients versus BR patients (RR = 1.10; 95% CI 0.89–1.35; P = 0.37), respectively.

Conclusions

Our study showed that there were no statistically significant differences concerning the occurrence of depressive symptoms in breast cancer patients as a consequence of TM, BCS or BR at mean time more than 1‐year term postoperatively.
Biclustering by sparse canonical correlation analysis
Authors: Pimentel Harold , Hu Zhiyue , Huang Haiyan
Published: February 2018

Background

Developing appropriate computational tools to distill biological insights from large‐scale gene expression data has been an important part of systems biology. Considering that gene relationships may change or only exist in a subset of collected samples, biclustering that involves clustering both genes and samples has become in‐creasingly important, especially when the samples are pooled from a wide range of experimental conditions.

Methods

In this paper, we introduce a new biclustering algorithm to find subsets of genomic expression features (EFs) (e.g., genes, isoforms, exon inclusion) that show strong “group interactions” under certain subsets of samples. Group interactions are defined by strong partial correlations, or equivalently, conditional dependencies between EFs after removing the influences of a set of other functionally related EFs. Our new biclustering method, named SCCA‐BC, extends an existing method for group interaction inference, which is based on sparse canonical correlation analysis (SCCA) coupled with repeated random partitioning of the gene expression data set.

Results

SCCA‐BC gives sensible results on real data sets and outperforms most existing methods in simulations. Software is available at https://github.com/pimentel/scca‐bc.

Conclusions

SCCA‐BC seems to work in numerous conditions and the results seem promising for future extensions. SCCA‐BC has the ability to find different types of bicluster patterns, and it is especially advantageous in identifying a bicluster whose elements share the same progressive and multivariate normal distribution with a dense covariance matrix.
The cost of Alzheimer's disease in China and re‐estimation of costs worldwide
Authors: Jia Jianping , Wei Cuibai , Chen Shuoqi , Li Fangyu , Tang Yi , Qin Wei , Zhao Lina , Jin Hongmei , Xu Hui , Wang Fen , Zhou Aihong , Zuo Xiumei , Wu Liyong , Han Ying , Han Yue , Huang Liyuan , Wang Qi , Li Dan , Chu Changbiao , Shi Lu , Gong Min , Du Yifeng , Zhang Jiewen , Zhang Junjian , Zhou Chunkui , Lv Jihui , Lv Yang , Xie Haiqun , Ji Yong , Li Fang , Yu Enyan , Luo Benyan , Wang Yanjiang , Yang Shanshan , Qu Qiumin , Guo Qihao , Liang Furu , Zhang Jintao , Tan Lan , Shen Lu , Zhang Kunnan , Zhang Jinbiao , Peng Dantao , Tang Muni , Lv Peiyuan , Fang Boyan , Chu Lan , Jia Longfei , Gauthier Serge
Published: February 2018

Introduction

The socioeconomic costs of Alzheimer's disease (AD) in China and its impact on global economic burden remain uncertain.

Methods

We collected data from 3098 patients with AD in 81 representative centers across China and estimated AD costs for individual patient and total patients in China in 2015. Based on this data, we re‐estimated the worldwide costs of AD.

Results

The annual socioeconomic cost per patient was US $19,144.36, and total costs were US $167.74 billion in 2015. The annual total costs are predicted to reach US $507.49 billion in 2030 and US $1.89 trillion in 2050. Based on our results, the global estimates of costs for dementia were US $957.56 billion in 2015, and will be US $2.54 trillion in 2030, and US $9.12 trillion in 2050, much more than the predictions by the World Alzheimer Report 2015.

Discussion

China bears a heavy burden of AD costs, which greatly change the estimates of AD cost worldwide.
Surgical and oncological short-term outcomes of prone extralevator abdominoperineal excision for low rectal cancer
Authors: Cesar Daniel , Araujo Rodrigo , Valadão Marcus , Linhares Eduardo , Meton Fernando , Jesus José Paulo de
Published: February 2018

Introduction In recent years, a standardized surgical approach for low rectal cancer was proposed and adopted in many centres. The extralevator abdominoperineal excision introduce an extensive resection of the pelvic floor and demonstrated superiority if the procedure is done in the prone jack-knife position, especially regarding intraoperative perforation and circumferential resections margins. The aim of this study is to evaluate the surgical and oncological short-term outcomes of prone extralevator abdominoperineal excision.

Methods All patients registered in our institution from January 2003 to January 2015 who underwent abdominoperineal resection or prone extralevator abdominoperineal excision for low rectal cancer after preoperative chemoradiation were retrospectively included from prospective maintained data base and were compared regarding surgical and oncological outcomes.

Results Eighty-nine patients underwent curative intent resections. Abdominoperineal resection was performed in 67 patients and prone extralevator abdominoperineal excision in 22 patients. There were no statistical significant differences between groups regarding pathological stage, median number of harvested lymph node, intraoperative perforation, circumferential resections margins involvement and recurrence rates. Surgical outcomes were statistically different between groups. Twenty-six patients (29%) developed perineal complications, 21% of the abdominoperineal resection patients and 55% of the prone extralevator abdominoperineal excision (p < 0.001). Most of these complications were due to delayed perineal wound healing (12.4%), and wound abscesses (4.5%). However, the readmission rate and median length of hospital stay was higher in the abdominoperineal resection group (p < 0.001).

Conclusion Prone extralevator abdominoperineal excision is comparable to standard abdominoperineal resection. It was associated to a decrease in length of hospital stay and readmission rate, although more perineal complications occurred. We cannot recommend it as a standard technique for all low rectal cancer. Notwithstanding, prone extralevator abdominoperineal excision can be considered a more radical approach when there is sphincter complex or levators muscles invasion.
An unusual case of interrupted cervical aortic arch associated with long segment coarctation of the descending thoracic aorta
Authors: Dey Mousam , Garg Naveen , Kumar Sunil
Published: February 2018

Interrupted aortic arch is a rare congenital anomaly in newborns and infants and is commonly associated with other cardiovascular anomalies. Here, we report an unusual case of type A interrupted cervical aortic arch associated with long segment coarctation of the descending thoracic aorta. Patent ductus arteriosus reconstituted the descending thoracic aorta. Proximal segments of the left common carotid and left subclavian arteries were atretic. Echocardiography-gated multidetector CT angiography not only identified the type of aortic arch interruption in the neonate but also delineated the exact anatomical details.
California’s Water Savings Dwindle When Drought Fears Subside
Authors: Underwood Emily
Published: February 2018

Policy changes and media attention affect how much water Californians use, as well as how long these behaviors prevail. Could public awareness shift behaviors toward long-term conservation?
Electrons dynamics control by shaping femtosecond laser pulses in micro/nanofabrication: modeling, method, measurement and application
Authors: Jiang Lan , Wang An-Dong , Li Bo , Cui Tian-Hong , Lu Yong-Feng
Published: February 2018

During femtosecond laser fabrication, photons are mainly absorbed by electrons, and the subsequent energy transfer from electrons to ions is of picosecond order. Hence, lattice motion is negligible within the femtosecond pulse duration, whereas femtosecond photon-electron interactions dominate the entire fabrication process. Therefore, femtosecond laser fabrication must be improved by controlling localized transient electron dynamics, which poses a challenge for measuring and controlling at the electron level during fabrication processes. Pump-probe spectroscopy presents a viable solution, which can be used to observe electron dynamics during a chemical reaction. In fact, femtosecond pulse durations are shorter than many physical/chemical characteristic times, which permits manipulating, adjusting, or interfering with electron dynamics. Hence, we proposed to control localized transient electron dynamics by temporally or spatially shaping femtosecond pulses, and further to modify localized transient materials properties, and then to adjust material phase change, and eventually to implement a novel fabrication method. This review covers our progresses over the past decade regarding electrons dynamics control (EDC) by shaping femtosecond laser pulses in micro/nanomanufacturing: (1) Theoretical models were developed to prove EDC feasibility and reveal its mechanisms; (2) on the basis of the theoretical predictions, many experiments are conducted to validate our EDC-based femtosecond laser fabrication method. Seven examples are reported, which proves that the proposed method can significantly improve fabrication precision, quality, throughput and repeatability and effectively control micro/nanoscale structures; (3) a multiscale measurement system was proposed and developed to study the fundamentals of EDC from the femtosecond scale to the nanosecond scale and to the millisecond scale; and (4) As an example of practical applications, our method was employed to fabricate some key structures in one of the 16 Chinese National S&T Major Projects, for which electron dynamics were measured using our multiscale measurement system.
Monolithically integrated stretchable photonics
Authors: Li Lan , Lin Hongtao , Qiao Shutao , Huang Yi-Zhong , Li Jun-Ying , Michon Jérôme , Gu Tian , Alosno-Ramos Carlos , Vivien Laurent , Yadav Anupama , Richardson Kathleen , Lu Nanshu , Hu Juejun
Published: February 2018

Mechanically stretchable photonics provides a new geometric degree of freedom for photonic system design and foresees applications ranging from artificial skins to soft wearable electronics. Here we describe the design and experimental realization of the first single-mode stretchable photonic devices. These devices, made of chalcogenide glass and epoxy polymer materials, are monolithically integrated on elastomer substrates. To impart mechanical stretching capability to devices built using these intrinsically brittle materials, our design strategy involves local substrate stiffening to minimize shape deformation of critical photonic components, and interconnecting optical waveguides assuming a meandering Euler spiral geometry to mitigate radiative optical loss. Devices fabricated following such design can sustain 41% nominal tensile strain and 3000 stretching cycles without measurable degradation in optical performance. In addition, we present a rigorous analytical model to quantitatively predict stress-optical coupling behavior in waveguide devices of arbitrary geometry without using a single fitting parameter.
Modulation of nuclear factor-kappa B activation by the endoplasmic reticulum stress sensor PERK to mediate estrogen-induced apoptosis in breast cancer cells
Authors: Fan Ping , Tyagi Amit K. , Agboke Fadeke A. , Mathur Rohit , Pokharel Niranjana , Jordan V. Craig
Published: February 2018

Stress responses are critical for estrogen (E2)-induced apoptosis in E2-deprived breast cancer cells. Nuclear factor-kappa B (NF-κB) is an important therapeutic target to prevent stress responses in chronic inflammatory diseases including cancer. However, whether E2 activates NF-κB to participate in stress-associated apoptosis in E2-deprived breast cancer cells is unknown. Here, we demonstrated that E2 differentially modulates NF-κB activity according to treatment time. E2 initially has significant potential to suppress NF-κB activation; it completely blocks tumor necrosis factor alpha (TNFα)-induced activation of NF-κB. We found that E2 preferentially and constantly enhances the expression of the adipogenic transcription factor CCAAT/enhancer binding protein beta (C/EBPβ), which is responsible for the suppression of NF-κB activation by E2 in MCF-7:5C cells. Interestingly, NF-κB p65 DNA-binding activity is increased when E2 is administered for 48 h, leading to the induction of TNFα and associated apoptosis. Blocking the nuclear translocation of NF-κB can completely prevent the induction of TNFα and apoptosis induced by E2. Further examination revealed that protein kinase RNA-like endoplasmic reticulum kinase (PERK), a stress sensor of unfolded protein response (UPR), plays an essential role in the late activation of NF-κB by E2. This modulation between PERK and NF-κB is mainly mediated by a stress responsive transcription factor, transducer and activator of transcription 3 (STAT3), independently of the classic canonical IκBα signaling pathway. Thus, inhibition of PERK kinase activity completely blocks the DNA binding of both STAT3 and NF-κB, thereby preventing induction of NF-κB-dependent genes and E2-induced apoptosis. All of these findings suggest that PERK is a key regulator to convey stress signals from the endoplasmic reticulum to the nucleus and illustrate a crucial role for the novel PERK/STAT3/NF-κB/TNFα axis in E2-induced apoptosis in E2-deprived breast cancer cells.
Aggregation-fragmentation and individual dynamics of active clusters
Authors: Ginot F. , Theurkauff I. , Detcheverry F. , Ybert C. , Cottin-Bizonne C.
Published: February 2018

A remarkable feature of active matter is the propensity to self-organize. One striking instance of this ability to generate spatial structures is the cluster phase, where clusters broadly distributed in size constantly move and evolve through particle exchange, breaking or merging. Here we propose an exhaustive description of the cluster dynamics in apolar active matter. Exploiting large statistics gathered on thousands of Janus colloids, we measure the aggregation and fragmentation rates and rationalize the resulting cluster size distribution and fluctuations. We also show that the motion of individual clusters is entirely consistent with a model positing random orientation of colloids. Our findings establish a simple, generic model of cluster phase, and pave the way for a thorough understanding of clustering in active matter.
Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T-PLL
Authors: Schrader A. , Crispatzu G. , Oberbeck S. , Mayer P. , Pützer S. , von Jan J. , Vasyutina E. , Warner K. , Weit N. , Pflug N. , Braun T. , Andersson E. I. , Yadav B. , Riabinska A. , Maurer B. , Ventura Ferreira M. S. , Beier F. , Altmüller J. , Lanasa M. , Herling C. D. , Haferlach T. , Stilgenbauer S. , Hopfinger G. , Peifer M. , Brümmendorf T. H. , Nürnberg P. , Elenitoba-Johnson K. S. J. , Zha S. , Hallek M. , Moriggl R. , Reinhardt H. C. , Stern M.-H. , Mustjoki S. , Newrzela S. , Frommolt P. , Herling M.
Published: February 2018

T-cell prolymphocytic leukemia (T-PLL) is a rare and poor-prognostic mature T-cell malignancy. Here we integrated large-scale profiling data of alterations in gene expression, allelic copy number (CN), and nucleotide sequences in 111 well-characterized patients. Besides prominent signatures of T-cell activation and prevalent clonal variants, we also identify novel hot-spots for CN variability, fusion molecules, alternative transcripts, and progression-associated dynamics. The overall lesional spectrum of T-PLL is mainly annotated to axes of DNA damage responses, T-cell receptor/cytokine signaling, and histone modulation. We formulate a multi-dimensional model of T-PLL pathogenesis centered around a unique combination of TCL1 overexpression with damaging ATM aberrations as initiating core lesions. The effects imposed by TCL1 cooperate with compromised ATM toward a leukemogenic phenotype of impaired DNA damage processing. Dysfunctional ATM appears inefficient in alleviating elevated redox burdens and telomere attrition and in evoking a p53-dependent apoptotic response to genotoxic insults. As non-genotoxic strategies, synergistic combinations of p53 reactivators and deacetylase inhibitors reinstate such cell death execution.
Mutations in CFAP43 and CFAP44 cause male infertility and flagellum defects in Trypanosoma and human
Authors: Coutton Charles , Vargas Alexandra S. , Amiri-Yekta Amir , Kherraf Zine-Eddine , Ben Mustapha Selima Fourati , Le Tanno Pauline , Wambergue-Legrand Clémentine , Karaouzène Thomas , Martinez Guillaume , Crouzy Serge , Daneshipour Abbas , Hosseini Seyedeh Hanieh , Mitchell Valérie , Halouani Lazhar , Marrakchi Ouafi , Makni Mounir , Latrous Habib , Kharouf Mahmoud , Deleuze Jean-François , Boland Anne , Hennebicq Sylviane , Satre Véronique , Jouk Pierre-Simon , Thierry-Mieg Nicolas , Conne Beatrice , Dacheux Denis , Landrein Nicolas , Schmitt Alain , Stouvenel Laurence , Lorès Patrick , El Khouri Elma , Bottari Serge P. , Fauré Julien , Wolf Jean-Philippe , Pernet-Gallay Karin , Escoffier Jessica , Gourabi Hamid , Robinson Derrick R. , Nef Serge , Dulioust Emmanuel , Zouari Raoudha , Bonhivers Mélanie , Touré Aminata , Arnoult Christophe , Ray Pierre F.
Published: February 2018

Spermatogenesis defects concern millions of men worldwide, yet the vast majority remains undiagnosed. Here we report men with primary infertility due to multiple morphological abnormalities of the sperm flagella with severe disorganization of the sperm axoneme, a microtubule-based structure highly conserved throughout evolution. Whole-exome sequencing was performed on 78 patients allowing the identification of 22 men with bi-allelic mutations in DNAH1 (n = 6), CFAP43 (n = 10), and CFAP44 (n = 6). CRISPR/Cas9 created homozygous CFAP43/44 male mice that were infertile and presented severe flagellar defects confirming the human genetic results. Immunoelectron and stimulated-emission-depletion microscopy performed on CFAP43 and CFAP44 orthologs in Trypanosoma brucei evidenced that both proteins are located between the doublet microtubules 5 and 6 and the paraflagellar rod. Overall, we demonstrate that CFAP43 and CFAP44 have a similar structure with a unique axonemal localization and are necessary to produce functional flagella in species ranging from Trypanosoma to human.
Discovery of a magnetic conductive interface in PbZr0.2Ti0.8O3 /SrTiO3 heterostructures
Authors: Zhang Yi , Xie Lin , Kim Jeongwoo , Stern Alex , Wang Hui , Zhang Kui , Yan Xingxu , Li Linze , Liu Henry , Zhao Gejian , Chi Hang , Gadre Chaitanya , Lin Qiyin , Zhou Yichun , Uher Ctirad , Chen Tingyong , Chu Ying-Hao , Xia Jing , Wu Ruqian , Pan Xiaoqing
Published: February 2018

Emergent physical properties often arise at interfaces of complex oxide heterostructures due to the interplay between various degrees of freedom, especially those with polar discontinuities. It is desirable to explore if these structures may generate pure and controllable spin currents, which are needed to attain unmatched performance and energy efficiency in the next-generation spintronic devices. Here we report the emergence of a spin-polarized two-dimensional electron gas (SP-2DEG) at the interface of two insulators, SrTiO3 and PbZr0.2Ti0.8O3. This SP-2DEG is strongly localized at the interfacial Ti atoms, due to the interplay between Coulomb interaction and band bending, and can be tuned by the ferroelectric polarization. Our findings open a door for engineering ferroelectric/insulator interfaces to create tunable ferroic orders for magnetoelectric device applications and provide opportunities for designing multiferroic materials in heterostructures.
Publisher Correction: Sumatran tiger survival threatened by deforestation despite increasing densities in parks
Authors: Luskin Matthew Scott , Albert Wido Rizki , Tobler Mathias W.
Published: February 2018

In the original version of the Article, reference 18 was incorrectly numbered as reference 30, and references 19 to 30 were incorrectly numbered as 18 to 29. These errors have now been corrected in the PDF and HTML versions of the manuscript.
USP35 regulates mitotic progression by modulating the stability of Aurora B
Authors: Park Jinyoung , Kwon Mi-Sun , Kim Eunice EunKyeong , Lee Hyunsook , Song Eun Joo
Published: February 2018

Although approximately 100 deubiquitinating enzymes (DUBs) are encoded in the human genome, very little is known about the DUBs that function in mitosis. Here, we demonstrate that DUB USP35 functions as a mitotic regulator by controlling the protein levels and downstream signaling of Aurora B and the depletion of USP35 eventually leads to several mitotic defects including cytokinesis failures. USP35 binds to and deubiquitinates Aurora B, and inhibits the APCCDH1-mediated proteasomal degradation of Aurora B, thus maintaining its steady-state levels during mitosis. In addition, the loss of USP35 decreases the phosphorylation of histone H3-Ser10, an Aurora B substrate. Finally, the transcription factor FoxM1 promotes the expression of USP35, as well as that of Aurora B, during the cell cycle. Our findings suggest that USP35 regulates the stability and function of Aurora B by blocking APCCDH1-induced proteasomal degradation, thereby controlling mitotic progression.
Inference of field reversed configuration topology and dynamics during Alfvenic transients
Authors: Romero J. A. , Dettrick S. A. , Granstedt E. , Roche T. , Mok Y.
Published: February 2018

Active control of field reversed configuration (FRC) devices requires a method to determine the flux surface geometry and dynamic properties of the plasma during both transient and steady-state conditions. The current tomography (CT) method uses Bayesian inference to determine the plasma current density distribution using both the information from magnetic measurements and a physics model in the prior. Here we show that, from the inferred current sources, the FRC topology and its axial stability properties are readily obtained. When Gaussian process priors are used and the forward model is linear, the CT solution involves non-iterative matrix operations and is then ideally suited for deterministic real-time applications. Because no equilibrium assumptions are used in this case, inference of plasma topology and dynamics up to Alfvenic frequencies then becomes possible. Inference results for the C-2U device exhibit self-consistency of motions and forces during Alfvenic transients, as well as good agreement with plasma imaging diagnostics.
Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly
Authors: Warren Wesley C. , García-Pérez Raquel , Xu Sen , Lampert Kathrin P. , Chalopin Domitille , Stöck Matthias , Loewe Laurence , Lu Yuan , Kuderna Lukas , Minx Patrick , Montague Michael J. , Tomlinson Chad , Hillier LaDeana W. , Murphy Daniel N. , Wang John , Wang Zhongwei , Garcia Constantino Macias , Thomas Gregg C. W. , Volff Jean-Nicolas , Farias Fabiana , Aken Bronwen , Walter Ronald B. , Pruitt Kim D. , Marques-Bonet Tomas , Hahn Matthew W. , Kneitz Susanne , Lynch Michael , Schartl Manfred
Published: February 2018

The extreme rarity of asexual vertebrates in nature is generally explained by genomic decay due to absence of meiotic recombination, thus leading to extinction of such lineages. We explore features of a vertebrate asexual genome, the Amazon molly, Poecilia formosa, and find few signs of genetic degeneration but unique genetic variability and ongoing evolution. We uncovered a substantial clonal polymorphism and, as a conserved feature from its interspecific hybrid origin, a 10-fold higher heterozygosity than in the sexual parental species. These characteristics seem to be a principal reason for the unpredicted fitness of this asexual vertebrate. Our data suggest that asexual vertebrate lineages are scarce not because they are at a disadvantage, but because the genomic combinations required to bypass meiosis and to make up a functioning hybrid genome are rarely met in nature.
Assessing cetacean surveys throughout the Mediterranean Sea: a gap analysis in environmental space
Authors: Mannocci Laura , Roberts Jason J. , Halpin Patrick N. , Authier Matthieu , Boisseau Oliver , Bradai Mohamed Nejmeddine , Cañadas Ana , Chicote Carla , David Léa , Di-Méglio Nathalie , Fortuna Caterina M. , Frantzis Alexandros , Gazo Manel , Genov Tilen , Hammond Philip S. , Holcer Draško , Kaschner Kristin , Kerem Dani , Lauriano Giancarlo , Lewis Tim , Notarbartolo di Sciara Giuseppe , Panigada Simone , Raga Juan Antonio , Scheinin Aviad , Ridoux Vincent , Vella Adriana , Vella Joseph
Published: February 2018

Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolationversusextrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months.
Common surgical procedures in pilonidal sinus disease: A meta-analysis, merged data analysis, and comprehensive study on recurrence
Authors: Stauffer V. K. , Luedi M. M. , Kauf P. , Schmid M. , Diekmann M. , Wieferich K. , Schnüriger B. , Doll D.
Published: February 2018

We systematically searched available databases. We reviewed 6,143 studies published from 1833 to 2017. Reports in English, French, German, Italian, and Spanish were considered, as were publications in other languages if definitive treatment and recurrence at specific follow-up times were described in an English abstract. We assessed data in the manner of a meta-analysis of RCTs; further we assessed non-RCTs in the manner of a merged data analysis. In the RCT analysis including 11,730 patients, Limberg & Dufourmentel operations were associated with low recurrence of 0.6% (95%CI 0.3–0.9%) 12 months and 1.8% (95%CI 1.1–2.4%) respectively 24 months postoperatively. Analysing 89,583 patients from RCTs and non-RCTs, the Karydakis & Bascom approaches were associated with recurrence of only 0.2% (95%CI 0.1–0.3%) 12 months and 0.6% (95%CI 0.5–0.8%) 24 months postoperatively. Primary midline closure exhibited long-term recurrence up to 67.9% (95%CI 53.3–82.4%) 240 months post-surgery. For most procedures, only a few RCTs without long term follow up data exist, but substitute data from numerous non-RCTs are available. Recurrence in PSD is highly dependent on surgical procedure and by follow-up time; both must be considered when drawing conclusions regarding the efficacy of a procedure.
Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma
Authors: Gharahkhani Puya , Burdon Kathryn P. , Cooke Bailey Jessica N. , Hewitt Alex W. , Law Matthew H. , Pasquale Louis R. , Kang Jae H. , Haines Jonathan L. , Souzeau Emmanuelle , Zhou Tiger , Siggs Owen M. , Landers John , Awadalla Mona , Sharma Shiwani , Mills Richard A. , Ridge Bronwyn , Lynn David , Casson Robert , Graham Stuart L. , Goldberg Ivan , White Andrew , Healey Paul R. , Grigg John , Lawlor Mitchell , Mitchell Paul , Ruddle Jonathan , Coote Michael , Walland Mark , Best Stephen , Vincent Andrea , Gale Jesse , RadfordSmith Graham , Whiteman David C. , Montgomery Grant W. , Martin Nicholas G. , Mackey David A , Wiggs Janey L. , MacGregor Stuart , Craig Jamie E. ,   The NEIGHBORHOOD consortium, Allingham R. Rand , Brilliant Murray , Budenz Donald L. , Fingert John H. , Gaasterland Douglas , Gaasterland Teresa , Hark Lisa , Hauser Michael , Igo Robert P. , Kraft Peter , Lee Richard K. , Lichter Paul R. , Liu Yutao , Moroi Syoko , Pericak-Vance Margaret , Realini Anthony , Rhee Doug , Richards Julia E. , Ritch Robert , Schuman Joel S. , Scott William K. , Singh Kuldev , Sit Arthur J. , Vollrath Douglas , Wollstein Gadi , Zack Donald J.
Published: February 2018

Open-angle glaucoma (OAG) is a major cause of blindness worldwide. To identify new risk loci for OAG, we performed a genome-wide association study in 3,071 OAG cases and 6,750 unscreened controls, and meta-analysed the results with GWAS data for intraocular pressure (IOP) and optic disc parameters (the overall meta-analysis sample size varying between 32,000 to 48,000 participants), which are glaucoma-related traits. We identified and independently validated four novel genome-wide significant associations within or near MYOF and CYP26A1, LINC02052 and CRYGS, LMX1B, and LMO7 using single variant tests, one additional locus (C9) using gene-based tests, and two genetic pathways - “response to fluid shear stress” and “abnormal retina morphology” - in pathway-based tests. Interestingly, some of the new risk loci contribute to risk of other genetically-correlated eye diseases including myopia and age-related macular degeneration. To our knowledge, this study is the first integrative study to combine genetic data from OAG and its correlated traits to identify new risk variants and genetic pathways, highlighting the future potential of combining genetic data from genetically-correlated eye traits for the purpose of gene discovery and mapping.
Chronic ETA antagonist reverses hypertension and impairment of structure and function of peripheral small arteries in aortic stiffening
Authors: Guo Xiaomei , Chen Huan , Han Ling , Haulon Stephan , Kassab Ghassan S.
Published: February 2018

Arterial stiffness may contribute to the pathogenesis of hypertension. The goal of this study is to elucidate the role of Endothelin-1 (ET-1) in aortic stiffening-induced hypertension through ETA receptor activation. An increase in aortic stiffness was created by use of a non-constrictive restraint, NCR on the abdominal aortic surface. A group of rats underwent aortic NCR or sham operation for 12 weeks and were then treated with ETA receptor antagonist BQ-123 for 3 weeks. We found that 12 weeks of aortic NCR significantly increased pulse and mean pressure and altered peripheral flow pattern, accompanied by an increased serum ET-1 level (p < 0.05). The increase in aortic stiffness (evidenced by an elevated pulse wave velocity) caused hypertrophic structural remodeling and decreased arterial compliance, along with an impaired endothelial function in peripheral small arteries. BQ-123 treatment only partially attenuated peripheral arterial hypertrophy and restored arterial compliance, but completely recovered endothelium function, and consequently restored local flow and lowered blood pressure. Our findings underscore the hemodynamic coupling between aortic stiffening and peripheral arterial vessels and flow dynamics through an ETA-dependent mechanism. ETA receptor blockade may have therapeutic potential for improving peripheral vessel structure and function in the treatment of aortic stiffness-induced hypertension.
Optimising the decellularization of human elastic cartilage with trypsin for future use in ear reconstruction
Authors: Rahman Shafiq , Griffin Michelle , Naik Anish , Szarko Matthew , Butler Peter E. M.
Published: February 2018

Decellularized scaffolds can induce chondrogenic differentiation of stem cells. This study compares different methods to optimise the decellularization of auricular cartilage. The process consisted of an initial 12 hour dry freeze thaw which froze the cartilage specimens in an empty tube at −20 °C. Samples were allowed to thaw at room temperature followed by submersion in phosphate buffer solution in which they were frozen at −20 °C for a 12 hour period. They were then allowed to thaw at room temperature as before. Protocol A subsequently involved subjecting specimens to both deoxyribonuclease and sodium deoxycholate. Protocol B and C were adaptations of this using 0.25% trypsin (7 cycles) and a 0.5 molar solution of ethylenediaminetetraacetic acid (3 hours for each cycle) respectively as additional steps. Trypsin accelerated the decellularization process with a reduction in DNA content from 55.4 ng/μL (native) to 17.3 ng/μL (P-value < 0.05) after 14 days. Protocol B showed a faster reduction in DNA content when compared with protocol A. In comparison to protocol C after 14 days, trypsin also showed greater decellularization with a mean difference of 11.7 ng/μL (P-value < 0.05). Histological analysis with H&E and DAPI confirmed depletion of cells at 14 days with trypsin.
Analysis of Epistasis among QTLs on Heading Date based on Single Segment Substitution Lines in Rice
Authors: Yang Zifeng , Jin Lingling , Zhu Haitao , Wang Shaokui , Zhang Guiquan , Liu Guifu
Published: February 2018

Heading date directly determines the planting districts and seasons, and thus plays an important role for producing and introducing of varieties. Limited to the materials and methodologies, analysis of epistasis still presents an obvious challenge. This thesis estimated effectively four types of epistatic components among dual QTLs on heading date based on eight single segment substitution lines (SSSLs) in rice. The results confirmed that they carried truly with heading date QTLs. Eleven pairs of QTLs were with 50.0% of significant epistatic effects, of which additive-additive, additive-dominance or dominance-additive, and dominance-dominance interaction components occupied 40.9%, 50.0% and 59.1%, respectively. One QTL always interacted with multiple QTLs in various components. Several characteristics of epistasis on heading date were found that 1) different epistatic components had almost consistent directions; 2) dominance-dominance epistasis was perhaps most important in the four epistatic components; 3) epistasis was mostly positive, delaying rice heading; and 4) all epistatic components were seasonal sensitive. Two flowering pathways were further confirmed via a network constructed among these QTLs. These results have further confirmed the prevalence of epistatic interactions, deepened the understanding of genetic and flowering mechanism, and excavated several advantageous genes on heading date in rice.
An in silico argument for mitochondrial microRNA as a determinant of primary non function in liver transplantation
Authors: Khorsandi Shirin Elizabeth , Salehi Siamak , Cortes Miriam , Vilca-Melendez Hector , Menon Krishna , Srinivasan Parthi , Prachalias Andreas , Jassem Wayel , Heaton Nigel
Published: February 2018

Mitochondria have their own genomic, transcriptomic and proteomic machinery but are unable to be autonomous, needing both nuclear and mitochondrial genomes. The aim of this work was to use computational biology to explore the involvement of Mitochondrial microRNAs (MitomiRs) and their interactions with the mitochondrial proteome in a clinical model of primary non function (PNF) of the donor after cardiac death (DCD) liver. Archival array data on the differential expression of miRNA in DCD PNF was re-analyzed using a number of publically available computational algorithms. 10 MitomiRs were identified of importance in DCD PNF, 7 with predicted interaction of their seed sequence with the mitochondrial transcriptome that included both coding, and non coding areas of the hypervariability region 1 (HVR1) and control region. Considering miRNA regulation of the nuclear encoded mitochondrial proteome, 7 hypothetical small proteins were identified with homolog function that ranged from co-factor for formation of ATP Synthase, REDOX balance and an importin/exportin protein. In silico, unconventional seed interactions, both non canonical and alternative seed sites, appear to be of greater importance in MitomiR regulation of the mitochondrial genome. Additionally, a number of novel small proteins of relevance in transplantation have been identified which need further characterization.