bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chopping techniques in cataract surgery
Authors: Lee Bryan S. , Chang David F. 
Published: December 2022

Purpose of review
To explain reasons for phaco chop, outline strategies for transitioning to chop, and summarize recent articles discussing chopping techniques.

Recent findings
New variations of phaco chop may help with managing dense cataracts. Studies generally continue to show similar phaco time between traditional manual chopping and femtosecond laser-assisted cataract surgery. A nitinol ring prechopper compresses the lens similarly to horizontal chopping, which may reduce phaco energy for certain cases.

Summary
Both vertical and horizontal chopping continue to demonstrate multiple advantages over other nucleus disassembly techniques.
Dilation devices in cataract surgery
Authors: Sarnicola Enrica , Sarnicola Caterina , Sarnicola Vincenzo 
Published: December 2022

Purpose of review
Cataract surgery in the setting of small pupil represent a major challenge and it is associated with a higher risk of complications. When pharmacologic pupil dilation fails, mechanical pupil expansion devices are needed to obtain and maintain sufficient intraoperative mydriasis. The purpose of this review is to assess the pupil expansion devices currently available.

Recent findings
A variety of pupil expansion devices are offered on the market. They differ for design, material, shape, size, cost, and easiness of insertion/removal, nonetheless they all seem to be effective in improving the pupil size and easing the cataract surgery.

Summary
Mechanical pupil expansion can be effectively achieved with a variety of devices, which are well tolerated and can facilitate cataract surgery in the setting of poor mydriasis.
Sequential intravesical gemcitabine and docetaxel therapy in patients with nonmuscle invasive bladder cancer: a systematic review and meta-analysis
Authors: Kawada Tatsushi , Yanagisawa Takafumi , Araki Motoo , Pradere Benjamin , Shariat Shahrokh F. 
Published: December 2022

Purpose of review
Shortages in intravesical Bacillus Calmette-Guérin (BCG) immunotherapy represent a challenge in the management of high-risk nonmuscle invasive bladder cancer (HR-NMIBC). This study aimed to review the efficacy and safety of intravesical gemcitabine (GEM) and docetaxel (DOCE) for BCG-naive and unresponsive HR-NMIBC.

Recent findings
We identified six studies eligible for quantitative analysis through a systematic search according to the Preferred Reporting Items for Systematic Review and Meta-analyses (PRISMA) statement. In the two studies in the BCG-naive setting, 1-year and 2-year pooled recurrence-free survival (RFS) were 86 and 84%, respectively. In the two studies in the BCG unresponsive setting, 6-month, 1-year and 2-year pooled high-grade recurrence-free survival (HG-RFS) were 80, 66 and 51%, respectively. Cumulative data from four studies revealed that 2.3% of patients could not complete induction therapy and 6.9% experienced treatment delay or dose reduction due to adverse events.

Summary
Despite the preliminary data and based on a small sample size, intravesical GEM/DOCE therapy is a highly promising combination yielding an effective and well tolerated alternative to BCG when indicated. Further large, well designed comparative studies with BCG are needed.
Prevention and Management of Chronic Postsurgical Pain and Persistent Opioid Use Following Solid Organ Transplantation: Experiences From the Toronto General Hospital Transitional Pain Service
Authors: Yu Hai Chuan , Kleiman Valery , Kojic Katarina , Slepian P. Maxwell , Cortes Henry , McRae Karen , Katznelson Rita , Huang Alex , Tamir Diana , Fiorellino Joseph , Ganty Praveen , Cote Nathalie , Kahn Michael , Mucsi Istvan , Selzner Nazia , Rozenberg Dmitry , Chaparro Cecilia , Rao Vivek , Cypel Marcelo , Ghanekar Anand , Kona Sharath , McCluskey Stuart , Ladak Salima , Santa Mina Daniel , Karkouti Keyvan , Katz Joel , Clarke Hance 
Published: December 2022

Background.
With >700 transplant surgeries performed each year, Toronto General Hospital (TGH) is currently one of the largest adult transplant centers in North America. There is a lack of literature regarding both the identification and management of chronic postsurgical pain (CPSP) after organ transplantation. Since 2014, the TGH Transitional Pain Service (TPS) has helped manage patients who developed CPSP after solid organ transplantation (SOT), including heart, lung, liver, and renal transplants.

Methods.
In this retrospective cohort study, we describe the association between opioid consumption, psychological characteristics of pain, and demographic characteristics of 140 SOT patients who participated in the multidisciplinary treatment at the TGH TPS, incorporating psychology and physiotherapy as key parts of our multimodal pain management regimen.

Results.
Treatment by the multidisciplinary TPS team was associated with significant improvement in pain severity and a reduction in opioid consumption.

Conclusions.
Given the risk of CPSP after SOT, robust follow-up and management by a multidisciplinary team should be considered to prevent CPSP, help guide opioid weaning, and provide psychological support to these patients to improve their recovery trajectory and quality of life postoperatively.
Effect of BNT162b2 antigen dosage on protection against SARS-CoV-2 omicron infection
Authors: Chemaitelly Hiam , Ayoub Houssein H. , Coyle Peter , Tang Patrick , Yassine Hadi M. , Al Thani Asmaa A. , Al-Khatib Hebah A. , Hasan Mohammad R. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Al-Romaihi Hamad Eid , Butt Adeel A. , Al-Thani Mohamed H. , Al-Khal Abdullatif , Bertollini Roberto , Abu-Raddad Laith J. 
Published: December 2022

AbstractBackgroundCoronavirus Disease 2019 (COVID-19) vaccine antigen dosage may affect protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but direct evidence to quantify this effect is lacking.MethodsA matched, retrospective, cohort study that emulated a randomized control trial was conducted in Qatar between February 3, 2022 and November 8, 2022, to provide a head-to-head, controlled comparison of protection induced by two antigen dosages of the BNT162b2 vaccine. The study compared incidence of omicron infection in the national cohort of adolescents 12 years of age who received the two-dose primary-series of the 30-µg BNT162b2 vaccine to that in the national cohort of adolescents 11 years of age who received the two-dose primary-series of the pediatric 10-µg BNT162b2 vaccine. Associations were estimated using Cox proportional-hazard regression models.ResultsAmong adolescents with no record of prior infection, cumulative incidence of infection was 6.0% (95% CI: 4.9-7.3%) for the 30-µg cohort and 7.2% (95% CI: 6.1-8.5%) for the 10-µg cohort, 210 days after the start of follow-up. Incidence during follow-up was dominated by omicron subvariants including, consecutively, BA.1/BA.2, BA.4/BA.5, BA.2.75*, and XBB. The adjusted hazard ratio comparing incidence of infection in the 30-µg cohort to the 10-µg cohort was 0.77 (95% CI: 0.60-0.98). Corresponding relative effectiveness was 23.4% (95% CI: 1.6-40.4%). Relative effectiveness was -3.3% (95% CI: -68.0-27.5%) among adolescents with a record of prior infection.ConclusionsThree-fold higher BNT162b2 dosage was associated with ∼25% higher protection against infection in infection-naïve adolescents of similar age. These findings may inform design of future COVID-19 vaccines and boosters for persons of different age groups.
Bridging Theory and Experiments of Priority Effects
Authors: Zou Heng-Xing , Rudolf Volker H. W. 
Published: December 2022

AbstractPriority effects play a key role in structuring natural communities, but considerable confusion remains about how they affect different ecological systems. Synthesizing previous studies, we show that this confusion arises because the mechanisms driving priority and the temporal scale at which they operate differ among studies, leading to divergent outcomes in species interactions and biodiversity patterns. We suggest grouping priority effects into two functional categories based on their mechanisms: “frequency-dependent” priority effects that arise from positive frequency dependence, and “trait-dependent” priority effects that arise from time-dependent changes in interacting traits. Through easy quantification of these categories from experiments, we can construct community models representing diverse biological mechanisms and interactions with priority effects, therefore better predicting their consequences across ecosystems.
The Hereditary and Epigenetic Fusion Gene Signatures of Multiple Myeloma
Authors: Fei Ling , Zhuo Noah , Zhuo Degen 
Published: December 2022

ABSTRACTFusion transcripts are thought to be somatic and associated with cancer. However, they have been observed in healthy tissues at high recurrent frequencies. We have used SCIF (SplicingCodesIdentifyFusion Transcripts) to analyze RNA-Seq data from 727 multiple myeloma (MM) patients of the MMRF CoMMpass Study.MTG1-SCART1, SCART1-CYP2E1, andTPM4-KLF2have been detected in 96.1%, 95.7%, and 92.2% of 727 MM patients and formed fusion gene signatures.MTG1-SCART1andSCART1-CYP2E1are read-through from the same locus and the two most recurrent epigenetic fusion genes (EFGs) out of 187 EFGs detected in ≥10% of 727 MM patients.TPM4-KLF2fusion gene, which was initially thought to be somatic, has been shown by a monozygotic twin genetic model to be a hereditary fusion gene (HFG) and the dominant genetic factor associated with MM. This work provides the first line of evidence that HFGs are the genetic factors and EFGs reflect the consequences between genetics and environments during development.
Stress Combinations and their Interactions in Plants Database (SCIPDb): A one-stop resource for understanding combined stress responses in plants
Authors: Priya Piyush , Patil Mahesh , Pandey Prachi , Singh Anupriya , Babu Vishnu Sudha , Senthil-Kumar Muthappa 
Published: December 2022

ABSTRACTWe have developedStressCombinations and theirInteractions inPlantsDatabase (SCIPDb;http://www.nipgr.ac.in/scipdb.php), a compendium and interactive platform offering information on both morpho-physio-biochemical (phenome) and molecular (transcriptome) responses of plants to different combinations of stresses. To delineate the effects of various stress combinations/categories on yield in major agricultural crops, global phenome data from 939 studies was analyzed and results showed that yield was affected to the greatest extent under the abiotic–abiotic stress category, followed by the biotic–biotic and abiotic–biotic stress categories. In the abiotic–abiotic stress category, drought–heat, heat–salinity, and ozone–UV are the major stress combinations causing high yield loss in barley, wheat, soybean, and quinoa crops. In the abiotic–biotic stress category, the salinity–weed stress combination causes highest yield loss in rice crop. In the biotic–biotic stress category, the nematode–fungus combination was most detrimental, causing considerable yield losses in potato, groundnut, and sugar beet crops. Transcriptome datasets from 36 studies hosted in SCIPDb identified novel genes. Thus far, these genes have not been known to play a role in combined stress. Integretome analysis under combined drought–heat stress pinpointed carbohydrate, amino acid, and energy metabolism pathways as the crucial metabolic, proteomic, and transcriptional components in plant tolerance to combined stress. These examples illustrate the application of SCIPDb in identifying novel genes and pathways involved in combined stress tolerance. Further, we showed the application of this database in identifying novel candidate genes and pathways for combined drought and pathogen stress tolerance in Arabidopsis and chickpea. To our knowledge, SCIPDb is the only publicly available platform that provides extensive information and paves the way for advancing mechanistic understanding of plant responses to combined stresses.
Recessive pathogenic variants inMCATcause combined oxidative phosphorylation deficiency
Authors: Webb Bryn D. , Nowinski Sara M. , Solmonson Ashley , Ganesh Jaya , Rodenburg Richard J. , Leandro João , Evans Anthony , Vu Hieu S. , Naidich Thomas P. , Gelb Bruce D. , DeBerardinis Ralph J. , Rutter Jared , Houten Sander M. 
Published: December 2022

AbstractMalonyl-CoA-acyl carrier protein transacylase (MCAT) is an enzyme involved in mitochondrial fatty acid synthesis (mtFAS) and catalyzes the transfer of the malonyl moiety of malonyl-CoA to the mitochondrial acyl carrier protein (ACP). Previously, we showed that loss-of-function of mtFAS genes, includingMcat, is associated with severe loss of electron transport chain (ETC) complexes in mouse immortalized skeletal myoblasts (Nowinski et al., 2020). Here, we report a proband presenting with hypotonia, failure to thrive, nystagmus, and abnormal brain MRI findings. Using whole exome sequencing, we identified biallelic variants inMCAT. Protein levels for NDUFB8 and COXII, subunits of complex I and IV respectively, were markedly reduced in lymphoblasts and fibroblasts, as well as SDHB for complex II in fibroblasts. ETC enzyme activities were decreased in parallel. Reexpression of wild-typeMCATrescued the phenotype in patient fibroblasts. This is the first report of a patient withMCATpathogenic variants and combined oxidative phosphorylation deficiency.
MembraneFold: Visualising transmembrane protein structure and topology
Authors: Gutierrez Santiago , Tyczynski Wojciech G. , Boomsma Wouter , Teufel Felix , Winther Ole 
Published: December 2022

AbstractBackgroundAlphaFold’s accuracy, which is often comparable to that of experimentally determined structures, has revolutionized protein structure research. Being a statistical method, AlphaFold implicitly infers the cellular environment, e.g. the cell membrane, from the protein sequence. Membrane protein topology prediction methods predict the cellular environment for each protein residue but not the structure. Current structure and topology tools thus provide complementary information.ResultsWe introduce the web server MembraneFold. MembraneFold combines protein structure (from an uploaded PDB file/AlphaFold DB/OmegaFold) and topology (DeepTMHMM) prediction in one server. The output is shown both as a structure with topology superimposed and as a sequence annotation. MembraneFold uses structures predicted by OmegaFold if neither a PDB file is uploaded nor the structure is available in AlphaFold DB.ConclusionMembraneFold is a user-friendly web server that provides practitioners with fast and accurate information about membrane proteins. It is available athttps://ku.biolib.com/MembraneFold/.
Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis
Authors: Zhang Le , Badai Jiayidaer , Wang Guan , Ru Xufang , Song Wenkai , You Yujie , He Jiaojiao , Huang Suna , Feng Hua , Chen Runsheng , Zhao Yi , Chen Yujie 
Published: December 2022

AbstractCentral nervous system (CNS) diseases, such as neurodegenerative disorders and brain diseases caused by acute injuries, are important yet challenging to study due to disease leisions’ locations and other complexities. Utilizing the powerful spatial transcriptome analysis together with novel algorithms we developed for the study, we report here for the first time a 3D trajectory map of gene expression changes in the brain following acute neural injury using a mouse model of intraventricular haemorrhage (IVH). IVH is a common and representative complication after various acute brain injuries with severe mortality and mobility implications. Our data identified three main 3D global pseudospace-time trajectory bundles which represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex induced by experimental intraventricular haematoma stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH. These results are informative in understanding the pathophysiological changes, including the spatial and temporal patterns of gene expression changes, in IVH patients after acute brain injuries and strategizing more effective clinical management regimens. The bioinformatics strategies will also be useful for the study of other CNS diseases.
Prospecting for zoonotic pathogens using targeted DNA enrichment
Authors: Enabulele Egie E. , Le Clec’h Winka , Roberts Emma K. , Thompson Cody W. , McDonough Molly M. , Ferguson Adam W. , Bradley Robert D. , Anderson Timothy J. C. , Platt Roy N. 
Published: December 2022

AbstractThere are over 60 zoonoses linked to small mammals, including some of the most devastating pathogens in human history. Meanwhile, millions of museum-archived tissues are available to understand natural history of these pathogens. Our goal is to maximize the value of museum collections for pathogen-based research using targeted sequence capture. To this end, we have generated a probe panel that includes 39,916, 80bp RNA probes targeting 32 pathogen groups, including bacteria, helminths, fungi, and protozoans. Lab generated, mock control samples show that we are capable of enriching targeted loci from pathogen DNA 2,882 to 6,746-fold. Further, we were able to identify bacterial species in museum-archived samples, includingBartonella, a known human zoonosis. These results show that probe-based enrichment of pathogens is a highly customizable and efficient method for identifying pathogens from museum-archived tissues.
Multiscale Mechanical Characterization and Computational Modeling of Fibrin Gels
Authors: Jimenez Julian M. , Tuttle Tyler , Guo Yifan , Miles Dalton , Buganza-Tepole Adrian , Calve Sarah 
Published: December 2022

AbstractFibrin is a naturally occurring protein network that forms a temporary structure to enable remodeling during wound healing. It is also a common tissue engineering scaffold because the structural properties can be controlled. However, to fully characterize the wound healing process and improve the design of regenerative scaffolds, understanding fibrin mechanics at multiple scales is necessary. Here, we present a strategy to quantify both the macroscale (1 – 10 mm) stress-strain response and the deformation of the mesoscale (10 – 1000 μm) network structure during unidirectional tensile tests. The experimental data is then used to inform a computational model to accurately capture the mechanical response of fibrin gels. Simultaneous mechanical testing and confocal microscopy imaging of fluorophore-conjugated fibrin gels revealed up to an 88% decrease in volume coupled with increase in volume fraction in deformed gels, and non-affine fiber alignment in the direction of deformation. Combination of the computational model with finite element analysis enabled us to predict the strain fields that were observed experimentally within heterogenous fibrin gels with spatial variations in material properties. These strategies can be expanded to characterize and predict the macroscale mechanics and mesoscale network organization of other heterogeneous biological tissues and matrices.Statement of SignificanceFibrin is a naturally-occurring scaffold that supports cellular growth and assembly ofde novotissue and has tunable material properties. Characterization of meso- and macro-scale mechanics of fibrin gel networks can advance understanding of the wound healing process and impact future tissue engineering approaches. Using structural and mechanical characteristics of fibrin gels, a theoretical and computational model that can predict multiscale fibrin network mechanics was developed. These data and model can be used to design gels with tunable properties.
Rapid, high-throughput phenotypic profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using benchtop flow cytometry
Authors: Anthony Colin J. , Lock Colin , Bentlage Bastian 
Published: December 2022

AbstractEndosymbiotic dinoflagellates (Family Symbiodiniaceae) are the primary producer of energy for many cnidarians, including corals. The intricate coral-dinoflagellate symbiotic relationship is becoming increasingly important under climate change, as its breakdown leads to mass coral bleaching and often mortality. Despite methodological progress, assessing the phenotypic traits of Symbiodiniaceaein-hospiteremains a complex task. Bio-optics, biochemistry, or “-omics” techniques are expensive, often inaccessible to investigators, or lack the resolution required to understand single-cell phenotypic states within endosymbiotic dinoflagellate assemblages. To help address this issue, we developed a protocol that collects information on cell autofluorescence, shape, and size to simultaneously generate phenotypic profiles for thousands of Symbiodiniaceae cells, thus revealing phenotypic variance of the Symbiodiniaceae assemblage to the resolution of single cells. As flow cytometry is adopted as a robust and efficient method for cell counting, integration of our protocol into existing workflows allows researchers to acquire a new level of resolution for studies examining the acclimation and adaptation strategies of Symbiodiniaceae assemblages.
The first homosporous lycophyte genome revealed the association between the dynamic accumulation of LTR-RTs and genome size variation
Authors: Yu Ji-Gao , Tang Jun-Yong , Wei Ran , Lan Mei-Fang , Xiang Rui-Chen , Xiang Qiao-Ping , Zhang Xian-Chun 
Published: December 2022

SUMMARYLycophytes and euphyllophytes (ferns and seed plants) are the two surviving lineages of vascular plants. The modern lycophytes (clubmosses) are herbaceous found either heterosporous (Isoetales and Selaginellales) or homosporous (Lycopodiales). The contrasting genome size between homosporous and heterosporous plants has long been an attractive topic. Most clubmosses are the resource plants of Huperzine A (HupA) which is invaluable for treating Alzheimer’s disease, but the evolutionary trajectory of which in land plants is unexplored. To better understand these fundamental questions, the genome data of a homosporous lycophyte is urgently required. We generated theLycopodium clavatumL. genome by applying a reformed pipeline for filtering out non-plant sequences. The obtained genome size is 2.30 Gb, distinguished in more than 85% repetitive elements of which 62% is LTR. Two whole genome duplications (WGDs) are rigorously detected. The content of LTR-RTs was more than ten times higher in homosporous lycophytes than heterosporous ones, although most appeared within one Mya. Then, we find that the LTR-RTs’ birth-death mode (a much greater birth and extremely slower death) contributes the accumulation of LTR-RTs resulting homosporous lycophyte genome expansion, while in heterosporous lycophytes, the mode is exactly the opposite. Furthermore, the five necessary enzymes of the HupA biosynthetic pathway were identified in theL. clavatumgenome, but absent in the other land plants. This decoded genome data will be a key cornerstone to elucidating the fundamental aspects of lycophyte biology and land plant evolution.