bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Multicenter Matched Comparison of Transanal and Robotic Total Mesorectal Excision for Mid and Low-rectal Adenocarcinoma
Authors: Lee Lawrence , de Lacy Borja , Gomez Ruiz Marcos , Liberman Alexander Sender , Albert Matthew R. , Monson John R. T. , Lacy Antonio , Kim Seon Hahn , Atallah Sam B. 
Published: June 2018

Objective:
To compare the quality of surgical resection of transanal total mesorectal excision (TA-TME) and robotic total mesorectal excision (R-TME).

Background:
Both TA-TME and R-TME have been advocated to improve the quality of surgery for rectal cancer below 10 cm from the anal verge, but there are little data comparing TA-TME and R-TME.

Methods:
Data of patients undergoing TA-TME or R-TME for rectal cancer below 10 cm from the anal verge and a sphincter-saving procedure from 5 high-volume rectal cancer referral centers between 2011 and 2017 were obtained. Coarsened exact matching was used to create balanced cohorts of TA-TME and R-TME. The main outcome was the incidence of poor-quality surgical resection, defined as a composite measure including incomplete quality of TME, or positive circumferential resection margin (CRM) or distal resection margin (DRM).

Results:
Out of a total of 730 patients (277 TA-TME, 453 R-TME), matched groups of 226 TA-TME and 370 R-TME patients were created. These groups were well-balanced. The mean tumor height from the anal verge was 5.6 cm (SD 2.5), and 70% received preoperative radiotherapy. The incidence of poor-quality resection was similar in both groups (TA-TME 6.9% vs R-TME 6.8%; P = 0.954). There were no differences in TME specimen quality (complete or near-complete TA-TME 99.1% vs R-TME 99.2%; P = 0.923) and CRM (5.6% vs 6.0%; P = 0.839). DRM involvement may be higher after TA-TME (1.8% vs 0.3%; P = 0.051).

Conclusions:
High-quality TME for patients with rectal adenocarcinoma of the mid and low rectum can be equally achieved by transanal or robotic approaches in skilled hands, but attention should be paid to the distal margin.
Evidence-based Reviews in Surgery
Authors: Kao Lillian S. , Ball Chad G. , Chaudhury Prosanto K. 
Published: June 2018

Question:
What are the clinical outcomes of early versus delayed laparoscopic cholecystectomy (LC) in acute cholecystitis with more than 72 hours of symptoms?

Design:
A randomized controlled trial.

Setting:
Single center at the University Hospital of Lausanne, Switzerland.

Patients:
Eighty-six patients were enrolled in the study that had symptoms of acute cholecystitis lasting more than 72 hours before admission.

Intervention:
Patients were randomly assigned to early LC or delayed LC.

Main Outcome:
Primary outcome was overall morbidity following initial diagnosis. Secondary outcomes included total length of stay, duration of antibiotic used, cost, and surgical outcome.

Results:
Overall morbidity was lower in early laparoscopic cholecystectomy (ELC) [6 (14%) vs 17 (39%) patients, P = 0.015]. Median total length of stay (4 vs 7 days, P < 0.001) and duration of antibiotic therapy (2 vs 10 days, P < 0.001) were shorter in the ELC group. Total hospital costs were lower in ELC (9349€ vs 12,361€, P = 0.018). Operative time and postoperative complications were similar (91 vs 88 minutes; P = 0.910) and (15% vs 17%; P = 1.000), respectively.

Conclusions:
ELC for acute cholecystitis even beyond 72 hours of symptoms is safe and associated with less overall morbidity, shorter total hospital stay, and duration of antibiotic therapy, as well as reduced cost compared with delayed cholecystectomy.
High Compliance to an Enhanced Recovery Pathway for Patients ≥65 Years Undergoing Major Small and Large Intestinal Surgery Is Associated With Improved Postoperative Outcomes
Authors: Owodunni Oluwafemi P. , Hampton Jessica , Bettick Dianne , Sateri Sara , Magnuson Thomas , Wick Elizabeth , Psoter Kevin J. , Gearhart Susan L. 
Published: June 2018

Objective:
This study was performed to evaluate compliance to an Enhanced Recovery Pathway (ERP) among patients ≥65 years and determine the effect of compliance on postoperative outcomes.

Summary Background Data:
ERPs improve postoperative outcomes in patients undergoing major surgery. Given the inherent decline of the older surgical patient, the benefit of an ERP in this population has been questioned.

Methods:
Patients undergoing major small and large intestinal surgery prior to and following ERP implementation at the Johns Hopkins Medical Institutions were entered into the ACS-NSQIP database. Outcomes included ERP compliance rates, complications, length of stay (LOS), and 30-day readmission rates were determined for older patients.

Results:
Nine hundred seventy-four patients (693 < 65 yrs and 281 ≥ 65 yrs) were included. Of those ≥ 65 years, 142 (51%) were entered prior to and 139 (49%) were entered following ERP implementation. More ERP than pre-ERP patients underwent laparoscopic procedures (45.3% vs. 32.4%, P = 0.02), had disseminated malignancies (9.4% vs. 2.8%, P = 0.03), and smoked (14.4% vs. 4.9%, P = 0.01). Overall compliance was 74.5%, and 47% of older ERP patients achieved high compliance (≥75% compliance with ERP variables). High compliance was associated with a 30% decrease LOS (IRR: 0.7 P = 0.001) and 60% decrease in major (CD ≥ II) complications (OR: 0.4 P = 0.05).

Conclusion:
LOS and complication rates following implementation of an ERP were significantly improved in highly compliant elderly patients. Interventions to further improve outcomes should target decreasing variability by increasing individual compliance with an effective clinical pathway.
HaploBlocker: Creation of subgroup specific haplotype blocks and libraries
Authors: Pook Torsten , Schlather Martin , de los Campos Gustavo , Mayer Manfred , Schoen Chris Carolin , Simianer Henner 
Published: June 2018

ABSTRACTThe concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction. We propose a novel approach (“HaploBlocker”) for defining and inferring haplotype blocks that focuses on linkage instead of the commonly used population-wide measures of linkage disequilibrium. We define a haplotype block as a sequence of genetic markers that has a predefined minimum frequency in the population and only haplotypes with a similar sequence of markers are considered to carry that block, effectively screening a dataset for group-wise identity-by-descent. From these haplotype blocks we construct a haplotype library that represents a large proportion of genetic variability with a limited number of blocks. Our method is implemented in the associated R-package HaploBlocker and provides flexibility to not only optimize the structure of the obtained haplotype library for subsequent analyses, but is also able to handle datasets of different marker density and genetic diversity. By using haplotype blocks instead of SNPs, local epistatic interactions can be naturally modelled and the reduced number of parameters enables a wide variety of new methods for further genomic analyses such as genomic prediction and the detection of selection signatures. We illustrate our methodology with a dataset comprising 501 doubled haploid lines in a European maize landrace genotyped at 501’124 SNPs. With the suggested approach, we identified 2’991 haplotype blocks with an average length of 2’685 SNPs that together represent 94% of the dataset.
Recapture rates and habitat associations of White-faced Darter Leucorhinnia dubia on Fenn’s and Whixall Moss, Shropshire, UK
Authors: Davies Rachel , Hardenberg Achaz von , Geary Matthew 
Published: June 2018

AbstractLand-use change and habitat loss are important drivers of biodiversity decline at both global and local scales. To protect species from the impacts of land-use change it is important to understand the population dynamics and habitat associations across these scales. Here we present an investigation into the survival and habitat preferences of White-faced Darter (Leucorrhinia dubia) at the local scale at Fenn’s and Whixall Moss, Shropshire, UK. We used capture-mark-recapture methods to investigate survival and used sightings of individual dragonflies along with habitat data to investigate habitat preference. We found that survival between capture-visits was very low and that White-faced Darter show a clear preference for the open moss habitat on this site. In both cases, we found that the detectability either through sightings or recaptures was potentially very low and suggest that this should be taken into account in future analyses. We suggest that this could be achieved by encouraging recorders to submit complete lists and to repeat visits to sites.
Childhood Cerebellar Tumors Mirror Conserved Fetal Transcriptional Programs
Authors: Vladoiu Maria C , El-Hamamy Ibrahim , Donovan Laura K , Farooq Hamza , Holgado Borja L , Ramaswamy Vijay , Mack Stephen C , Lee John JY , Kumar Sachin , Przelicki David , Michealraj Antony , Juraschka Kyle , Skowron Patryk , Luu Betty , Suzuki Hiromichi , Morrissy A Sorana , Cavalli Florence MG , Garzia Livia , Daniels Craig , Wu Xiaochong , Qazi Maleeha A , Singh Sheila K , Chan Jennifer A , Marra Marco A , Malkin David , Dirks Peter , Pugh Trevor , Notta Faiyaz , Kleinman Claudia L , Joyner Alexandra , Jabado Nada , Stein Lincoln , Taylor Michael D. 
Published: June 2018

SummaryThe study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. Sonic Hedgehog medulloblastoma transcriptionally mirrors the granule cell hierarchy as expected, whereas Group 3 medulloblastoma resemble Nestin+ve stem cells, Group 4 medulloblastomas resemble unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumors demonstrates that many bulk tumors contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumors as a disorder of early brain development, and provide a proximate explanation for the peak incidence of cerebellar tumors in early childhood.
Neuropathological correlates and genetic architecture of microglial activation in elderly human brain
Authors: Felsky Daniel , Roostaei Tina , Nho Kwangsik , Risacher Shannon L. , Bradshaw Elizabeth M. , Petyuk Vlad , Schneider Julie A , Saykin Andrew , Bennett David A. , De Jager Philip L. 
Published: June 2018

AbstractMicroglia, the resident immune cells of the brain, have important roles in brain health. However, little is known about the regulation and consequences of microglial activation in the aging human brain. We assessed the effect of microglial activation in the aging human brain by calculating the proportion of activated microglia (PAM), based on morphologically defined stages of activation in four regions sampled postmortem from up to 225 elderly individuals. We found that cortical and not subcortical PAM measures were strongly associated with β-amyloid, tau-related neuropathology, and rates of cognitive decline. Effect sizes for PAM measures are substantial, comparable to that of APOE ɛ4, the strongest genetic risk factor for Alzheimer’s disease. Mediation modeling suggests that PAM accelerates accumulation of tau pathology leading to cognitive decline, supporting an upstream role for microglial activation in Alzheimer’s disease. Genome-wide analyses identified a common variant (rs2997325) influencing cortical PAM that also affected in vivo microglial activation measured by positron emission tomography using [11C]-PBR28 in an independent cohort. Finally, we identify overlaps of PAM’s genetic architecture with those of Alzheimer’s disease, educational attainment, and several other traits.
Two-step binding kinetics of tRNAGly by the glyQS T-box riboswitch and its regulation by T-box structural elements
Authors: Zhang Jiacheng , Chetnani Bhaskar , Cormack Eric D. , Liu Wei , Mondragón Alfonso , Fei Jingyi 
Published: June 2018

ABSTRACTT-box riboswitches are cis-regulatory RNA elements that regulate mRNAs encoding for aminoacyl tRNA synthetases or proteins involved in amino acid biosynthesis and transport. Rather than using small molecules as their ligands, as do most riboswitches, T-box riboswitches uniquely bind tRNA and sense their aminoacylated state. Whereas the anticodon and elbow regions of the tRNA interact with Stem I, located in the 5’ portion of the T-box, sensing of the aminoacylation state involves direct binding of the NCCA sequence at the tRNA 3’ end to the anti-terminator sequence located in the 3’ portion of the T-box. However, the kinetic trajectory that describes how each of these interactions are established temporally during tRNA binding remains unclear. Using singlemolecule fluorescence resonance energy transfer (smFRET), we demonstrate that tRNA binds to the riboswitch in a two-step process, first with anticodon recognition followed by NCCA binding, with the second step accompanied by an inward motion of the 3’ portion of the T-box riboswitch relative to Stem I. By using site-specific mutants, we further show that the T-loop region of the T-box significantly contributes to the first binding step, and that the K-turn region of the T-box influences both binding steps, but with a more dramatic effect on the second binding step. Our results set up a kinetic framework describing tRNA binding by T-box riboswitches and highlight the important roles of several T-box structural elements in regulating each binding step.SIGNIFICANCEBacteria commonly use riboswitches, cis-regulatory RNA elements, to regulate the transcription or translation of the mRNAs upon sensing signals. Unlike small molecule binding riboswitches, T-box riboswitches bind tRNA and sense their aminoacylated state. T-box modular structural elements that recognize different parts of a tRNA have been identified, however, how each of these interactions is established temporally during tRNA binding remains unclear. Our study reveals that tRNA binds to the riboswitch in a two-step mechanism, with anticodon recognition first, followed by binding to the NCCA sequence at the 3’ end of the tRNA with concomitant conformational changes in the T-box. Our results also highlight the importance of the modular structural elements of the T-box in each of the binding steps.
Acute inflammation sensitizes knee-innervating sensory neurons and decreases mouse digging behavior in a TRPV1-dependent manner
Authors: Chakrabarti Sampurna , Pattison Luke A. , Singhal Kaajal , Hockley James R.F. , Callejo Gerard , John Smith Ewan St. 
Published: June 2018

AbstractOngoing, spontaneous pain is characteristic of inflammatory joint pain and reduces an individual’s quality of life. To understand the neural basis of inflammatory joint pain, we made a unilateral knee injection of complete Freund’s adjuvant (CFA) in mice, which reduced their natural digging behavior. We hypothesized that sensitization of knee-innervating dorsal root ganglion (DRG) neurons underlies this altered behavior. To test this hypothesis, we performed electrophysiological recordings on retrograde labelled knee-innervating primary DRG neuron cultures and measured their responses to a number of electrical and chemical stimuli. We found that 24-hours after CFA-induced knee inflammation, knee neurons show a decreased action potential generation threshold, as well as increased GABA and capsaicin sensitivity, but have unaltered acid sensitivity. The inflammation-induced sensitization of knee neurons persisted for 24-hours in culture, but was not observed after 48-hours in culture. Through immunohistochemistry, we showed that the increased knee neuron capsaicin sensitivity correlated with enhanced expression of the capsaicin receptor, transient receptor potential vanilloid 1 (TRPV1) in knee-innervating neurons of the CFA-injected side. We also observed an increase in the co-expression of TRPV1 with tropomyosin receptor kinase A (TrkA), which is the receptor for nerve growth factor (NGF), suggesting that NGF partially induces the increased TRPV1 expression. Lastly, we found that systemic administration of the TRPV1 antagonist A-425619 reversed the decrease in digging behavior induced by CFA injection, further confirming the role of TRPV1, expressed by knee neurons, in acute inflammatory joint pain.
Exploration in the presence of mother in typically and non-typically developing pre-walking human infants
Authors: Frostig T. , Alonim H. , Scheingesicht G. , Benjamini Y. , Golani I. 
Published: June 2018

AbstractUsing an arsenal of tools previously developed for the study of origin-related exploration in animals, we compared exploration of human pre-walking Typically-Developing (TD) and Non-Typically Developing (NTD) infants in the presence of mother. The NTD infants had been referred to a center for the treatment of autism by pediatric neurologists and expert clinicians. Using computational analysis we document in TD infants a phylogenetic ancient behavior: origin-related exploration. Strikingly, while the TD infants exhibited excursions in reference to mother and deep engagement with mother when visiting her, the NTD infants tended to avoid mother’s place, performing few if any excursions, and exhibiting shallow engagement with mother. Given the pervasiveness of origin-related exploration in invertebrates, vertebrates, and primates, we now face a challenge to find an animal model that will exhibit active exploration while ignoring or suppressing the return to the origin, be it a mother or any other safe haven.
Genome-wide characterization, evolutionary analysis of WRKY genes in Cucurbitaceae species and assessment of its roles in resisting to powdery mildew disease
Authors: Jiao Zigao , Sun Jianlei , Wang Chongqi , Dong Yumei , Xiao Shouhua , Gao Xuli , Cao Qiwei , Li Libin , Li Wendong , Gao Chao 
Published: June 2018

AbstractThe WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon (Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.
Sequence analysis and confirmation of type IV pili-associated proteins PilY1, PilW and PilV in Acidithiobacillus thiooxidans
Authors: Alfaro-Saldaña Elvia , Hernández-Sánchez O. Araceli , Soberano-Patrón Araceli , Astello-García Marizel , Méndez-Cabañas J. Alfredo , García-Meza J. Viridiana 
Published: June 2018

AbstractAcidithiobacillus thiooxidans is an acidophilic chemolithoautotrophic bacterium widely used in the mining industry due to its metabolic sulfur-oxidizing capability. The biooxidation of sulfide minerals is enhanced through the attachment of A. thiooxidans cells to the mineral surface. The Type IV pili (TfP) of At. thiooxidans may play an important role in the bacteria attachment, since among other functions, TfP play a key adhesive role in the attachment to and colonization of different surfaces. In this work, we reported for the first time the confirmed mRNA sequences of three TfP proteins from At. thiooxidans, the protein PilY1 and the TfP pilins PilW and PilV. The nucleotide sequences of these TfP proteins show changes of some nucleotide positions with respect to the corresponding annotated sequences. The bioinformatic analyses and 3D-modeling of protein structures sustain their classification as TfP proteins, as structural homologs of the corresponding proteins of P. aeruginosa, results that sustain the role of PilY1, PilW and PilV in pili assembly. Also, that PilY1 comprises the conserved Neisseria-PilC (superfamily) domain of the tip-associated adhesin, while PilW of the superfamily of putative TfP assembly proteins and PilV belongs to the superfamily of TfP assembly protein. Also, the analyses suggested the presence of specific functional domains involved in adhesion, energy transduction and signaling functions. The phylogenetic analysis indicated that the PilY1 of Acidithiobacillus genus forms a cohesive group linked with iron- and/or sulfur-oxidizing microorganisms from acid mine drainage or mine tailings. This work enriches knowledge regarding colonization, adhesion and biooxidation of inorganic sulfurs by A. thiooxidans.
Spacecraft localization by indirect linear measurements from a single antenna
Authors: Hajiyev Chingiz , Sofyali Ahmet 
Published: June 2018

Purpose
The purpose of this paper is to present a two-stage approach for estimation of spacecraft’s position and velocity by indirect linear measurements from a single antenna.

Design/methodology/approach
In the first stage, direct nonlinear antenna measurements are transformed to linear x-y-z coordinate measurements of spacecraft’s position, and statistical characteristics of orbit determination errors are analyzed. Variances of orbit parameters’ errors are chosen as the accuracy criteria. In the second stage, the outputs of the first stage are improved by the designed Extended Kalman Filter for estimation of the spacecraft’s position and velocity on indirect linear x-y-z measurements.

Findings
The complex content of the measurement matrix in the conventional method causes periodic singularities in simulation results. In addition, the convergence of the filter using direct measurements is highly dependent on the initialization parameters’ values due to the nonlinear partial derivatives in the Jacobian measurement matrix. The comparison of the accuracy of both methods shows that the estimation by using indirect measurements reduces the absolute estimation errors. The simulation results show that the proposed two-stage procedure performs both with better estimation accuracy and better convergence characteristics. The method based on indirect measurements provides an unnoticeably short transient duration.

Practical implications
The proposed method can be recommended for satellite orbit estimation regarding its presented superiorities.

Originality/value
Inputting the single antenna measurements to the filter indirectly results in a quite simpler measurement matrix. As a result, the convergence of the filter is faster and estimation errors are lower.