bluuebunny/crossref_metadata_2025_split huggingface dataset:
Robotic-assisted radical cystectomy with complete intracorporal diversion: Initial experience in a tertiary teaching hospital
Authors: He Yilu , Shanmugasundaram Ramesh , Hana Bishoy , McCombie Steve P , Bhoopathy Varun , Myint Michael , Arianayagam Mohan , Canagasingham Betram , Ferguson Richard , Goolam Ahmed S , Jeffery Nicola , Khadra Mohamed , Ko Raymond , Varol Celi , Winter Matthew 
Published: August 2021

Objective: The aim of this study was to report the outcomes from robotic-assisted radical cystectomy (RARC) at an Australian public teaching hospital since the introduction of this technique in 2012. Methods: A retrospective analysis was conducted on perioperative and pathological outcomes from a consecutive series of 43 patients who underwent RARC for bladder cancer between 2012 and 2020 at Nepean Public Hospital. Results: Median operative time was 352 minutes for 32 (74.4%) patients undergoing construction of an ileal conduit, 499 minutes for nine (20.9%) patients undergoing construction of a neo-bladder and 239 minutes for two (4.7%) patients undergoing percutaneous urostomy. Median estimated blood loss was 500 mL, and median length of stay was 12 days. Complications within 60 days of any grade occurred in 63.4% of patients, and major complications (Clavien–Dindo ⩾Grade III) occurred in 20.9% of patients. The median number of lymph nodes removed was 17. Positive surgical margins occurred in 11.6% of patients overall, all in patients with T3 and above disease. Neo-adjuvant chemotherapy was utilised in 34.9% of patients overall and in 71.4% of patients with muscle-invasive urothelial cancer. Conclusion: The perioperative and pathological outcomes from RARC at our institution are comparable to the international literature. Level of evidence Level 4.
Insulin amyloid fibrils interact directly with the NLRP3, resulting in inflammasome activation and pyroptotic cell death
Authors: Mori Wakako , Kaneko Naoe , Nakanishi Ayaka , Zako Tamotsu , Masumoto Junya 
Published: August 2021

Introduction Nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3), an intracellular pattern recognition receptor, recognizes various pathogen-associated molecular pattern and/or damage-associated molecular pattern molecules to constitute inflammasome that act as an interleukin (IL)-1β processing platform. Injected insulin is reported to induce focal amyloidosis and the formation of subcutaneous lumps called insulin balls, but the formation of subcutaneous lumps and the underlying cytotoxic mechanism has not been elucidated. Methods Amyloid formation was evaluated by thioflavin T spectroscopic assay and scanning electron microscopy. Binding between insulin amyloid fibrils and NLRP3 was evaluated by immunoprecipitation followed by native polyacrylamide gel electrophoresis. Inflammasome activation was evaluated by immunofluorescence speck formation called “ASC speck” and Western blotting. IL-1β secretion in culture supernatants of peripheral blood mononuclear cells was evaluated by enzyme-linked immunosorbent assay. Cytotoxicity was measured by lactate dehydrogenase release assay. Results Insulin amyloid fibrils interact directly with NLRP3, resulting in NLRP3 inflammasome activation and pyroptotic cell death. Conclusion Insulin ball formation and cytotoxicity may be associated with NLRP3 inflammasome activation followed by pyroptotic cell death.
Muscle Degeneration Induced by Sequential Release and Denervation of the Rotator Cuff Tendon in Sheep
Authors: Wieser Karl , Grubhofer Florian , Hasler Anita , Götschi Tobias , Beeler Silvan , Meyer Dominik , Rechenberg Brigitte von , Gerber Christian 
Published: August 2021

Background: In a sheep rotator cuff model, tenotomy predominantly induces fatty infiltration, and denervation induces mostly muscle atrophy. In clinical practice, myotendinous retraction after tendon tear or lateralization after tendon repair tear may lead to traction injury of the nerve. Purpose/Hypothesis: To analyze whether an additional nerve lesion during rotator cuff repair leads to further degeneration of the rotator cuff muscle in the clinical setting. We hypothesized that neurectomy after tendon tear would increase atrophy as well as fatty infiltration and that muscle paralysis after neurectomy would prevent myotendinous retraction after secondary tendon release. Study Design: Controlled laboratory study. Methods: Twelve Swiss alpine sheep were used for this study. For the 6 sheep in the tenotomy/neurectomy (T/N) group, the infraspinatus tendon was released; 8 weeks later, the suprascapular nerve was transected. For the 6 sheep in the neurectomy/tenotomy (N/T) group, neurectomy was performed, and the infraspinatus was tenotomized 8 weeks later. All sheep were sacrificed after 16 weeks. Magnetic resonance imaging (MRI) was performed before the first surgery (baseline) and then after 8 and 16 weeks. The MRI data were used to assess muscle volume, fat fraction, musculotendinous retraction, pennation angle, and muscle fiber length of the infraspinatus muscle. Results: Three sheep (2 in the T/N and 1 in the N/T group) had to be excluded because the neurectomy was incomplete. After 8 weeks, muscle volume decreased significantly less in the T/N group (73% ± 2% of initial volume vs 52% ± 7% in the N/T group; P < .001). After 16 weeks, the mean intramuscular fat increase was higher in the T/N group (36% ± 9%) than in the N/T group (23% ± 6%), without reaching significance ( P = .060). After 16 weeks, the muscle volumes of the N/T (52% ± 8%) and T/N (49% ± 3%) groups were the same ( P = .732). Conclusion: Secondary neurectomy after tenotomy of a musculotendinous unit increases muscle atrophy. Tenotomy of a denervated muscle is associated with substantial myotendinous retraction but not with an increase of fatty infiltration to the level of the tenotomy first group. Clinical Relevance: Substantial retraction, which is associated with hitherto irrecoverable fatty infiltration, should be prevented, and additional neurogenic injury during repair should be avoided to limit the development of further atrophy.
Surgical management in retroperitoneal fibrosis: beyond ureterolysis
Authors: Venkatachalapathy Vigneswara Srinivasan Sockkalingam , Palathullil Datson George , Sam Dempsey Mohan , Abraham George Palathullil 
Published: August 2021

Abstract
Background
Retroperitoneal fibrosis can be associated with bilateral dense and extensive periureteral adhesions. When ureterolysis could not be successfully performed due to disease extent and severity, elaborate ureteral reconstructive procedures will be required.

Case presentation
A young male with retroperitoneal fibrosis presented with bilateral hydroureteronephrosis. The ureteral involvement was extensive and adhesions were dense. He was managed by laparoscopic boari flap ureteroneocystostomy on one renal unit and laparoscopic nephrectomy with renal autotransplantation on the other renal unit.

Conclusions
Ureterolysis is not feasible in all cases of retroperitoneal fibrosis. Extensive bilateral ureteral reconstruction without using intestinal segments is feasible. Minimally invasive surgical reconstructive procedures can be successfully employed in such scenarios also.
Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content
Authors: Kang Huimin , Zhao Di , Xiang Hai , Li Jing , Zhao Guiping , Li Hua 
Published: August 2021

AbstractBackgroundIn broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age.ResultsFirst, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism.ConclusionsOur study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.
Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
Authors: Smith Rachel L. , Goddard Amelia , Boddapati Arun , Brooks Steven , Schoeman Johan P. , Lack Justin , Leisewitz Andrew , Ackerman Hans 
Published: August 2021

AbstractBackgroundBabesia rossiis a leading cause of morbidity and mortality among the canine population of sub-Saharan Africa, but pathogenesis remains poorly understood. Previous studies ofB. rossiinfection were derived from clinical cases, in which neither the onset of infection nor the infectious inoculum was known. Here, we performed controlledB. rossiinoculations in canines and evaluated disease progression through clinical tests and whole blood transcriptomic profiling.ResultsTwo subjects were administered a low inoculum (104parasites) while three received a high (108parasites). Subjects were monitored for 8 consecutive days; anti-parasite treatment with diminazene aceturate was administered on day 4. Blood was drawn prior to inoculation as well as every experimental day for assessment of clinical parameters and transcriptomic profiles. The model recapitulated natural disease manifestations including anemia, acidosis, inflammation and behavioral changes. Rate of disease onset and clinical severity were proportional to the inoculum. To analyze the temporal dynamics of the transcriptomic host response, we sequenced mRNA extracted from whole blood drawn on days 0, 1, 3, 4, 6, and 8. Differential gene expression, hierarchical clustering, and pathway enrichment analyses identified genes and pathways involved in response to hemolysis, metabolic changes, and several arms of the immune response including innate immunity, adaptive immunity, and response to viral infection.ConclusionsThis work comprehensively characterizes the clinical and transcriptomic progression ofB. rossiinfection in canines, thus establishing a large mammalian model of severe hemoprotozoal disease to facilitate the study of host-parasite biology and in which to test novel anti-disease therapeutics. The knowledge gained from the study ofB. rossiin canines will not only improve our understanding of this emerging infectious disease threat in domestic dogs, but also provide insight into the pathobiology of human diseases caused byBabesiaandPlasmodiumspecies.
Transcriptomic analysis to elucidate the effects of high stocking density on grass carp (Ctenopharyngodon idella)
Authors: He Yan , Yu Hongyan , Zhao Honggang , Zhu Hua , Zhang Qingjing , Wang Anqi , Shen Yubang , Xu Xiaoyan , Li Jiale 
Published: August 2021

Abstract
Background
Grass carp (Ctenopharyngodon idella) is one of the most widely cultivated fishes in China. High stocking density can reportedly affect fish growth and immunity. Herein we performed PacBio long-read single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing to evaluate the effects of high stocking density on grass carp transcriptome.

Results
SMRT sequencing led to the identification of 33,773 genes (14,946 known and 18,827 new genes). From the structure analysis, 8,009 genes were detected with alternative splicing events, 10,219 genes showed alternative polyadenylation sites and 15,521 long noncoding RNAs. Further, 1,235, 962, and 213 differentially expressed genes (DEGs) were identified in the intestine, muscle, and brain tissues, respectively. We performed functional enrichment analyses of DEGs, and they were identified to be significantly enriched in nutrient metabolism and immune function. The expression levels of several genes encoding apolipoproteins and activities of enzymes involved in carbohydrate enzymolysis were found to be upregulated in the high stocking density group, indicating that lipid metabolism and carbohydrate decomposition were accelerated. Besides, four isoforms of grass carp major histocompatibility complex class II antigen alpha and beta chains in the aforementioned three tissue was showed at least a 4-fold decrease.

Conclusions
The results suggesting that fish farmed at high stocking densities face issues associated with the metabolism and immune system. To conclude, our results emphasize the importance of maintaining reasonable density in grass carp aquaculture.
Scattered migrating colony formation in the filamentous cyanobacterium, Pseudanabaena sp. NIES-4403
Authors: Yamamoto Hiroki , Fukasawa Yuki , Shoji Yu , Hisamoto Shumpei , Kikuchi Tomohiro , Takamatsu Atsuko , Iwasaki Hideo 
Published: August 2021

AbstractBackgroundBacteria have been reported to exhibit complicated morphological colony patterns on solid media, depending on intracellular, and extracellular factors such as motility, cell propagation, and cell-cell interaction. We isolated the filamentous cyanobacterium,Pseudanabaenasp. NIES-4403 (Pseudanabaena, hereafter), that forms scattered (discrete) migrating colonies on solid media. While the scattered colony pattern has been observed in some bacterial species, the mechanism underlying such a pattern still remains obscure.ResultsWe studied the morphology ofPseudanabaenamigrating collectively and found that this species forms randomly scattered clusters varying in size and further consists of a mixture of comet-like wandering clusters and disk-like rotating clusters. Quantitative analysis of the formation of these wandering and rotating clusters showed that bacterial filaments tend to follow trajectories of previously migrating filaments at velocities that are dependent on filament length. Collisions between filaments occurred without crossing paths, which enhanced their nematic alignments, giving rise to bundle-like colonies. As cells increased and bundles aggregated, comet-like wandering clusters developed. The direction and velocity of the movement of cells in comet-like wandering clusters were highly coordinated. When the wandering clusters entered into a circular orbit, they turned into rotating clusters, maintaining a more stable location. Disk-like rotating clusters may rotate for days, and the speed of cells within a rotating cluster increases from the center to the outmost part of the cluster. Using a mathematical modeling with simplified assumption we reproduced some features of the scattered pattern including migrating clusters.ConclusionBased on these observations, we propose thatPseudanabaenaforms scattered migrating colonies that undergo a series of transitions involving several morphological patterns. A simplified model is able to reproduce some features of the observed migrating clusters.
Emergence agitation after intraoperative neurolytic celiac plexus block with alcohol: a case report
Authors: Zhou Huixuan , Pan Yinbing , Liu Cunming , Sun Xiaodi 
Published: August 2021

Abstract
Background
Emergence agitation after general anesthesia may cause several undesirable events in the clinic during patient anesthesia recovery, and acute alcohol intoxication, while rare in surgery, is one of the risk factors.

Case presentation
A 66-year-old male patient was found to have pancreatic tail neoplasm upon computed tomography (CT) examination. The surgeon planned to resect the pancreatic tail under general anesthesia. However, the surgeon found extensive tumor metastasis in the abdominal cavity, and thus performed a neurolytic celiac plexus block (NCPB) with 40 ml 95% ethyl alcohol and finished the surgery in approximately 1 h. Twenty minutes later, the patient was extubated and developed significant emergence agitation in the postoperative care unit, characterized by restlessness, uncontrollable movements, confusion and disorientation. The patient was flushed and febrile with an alcohol smell in his breath and was unable to follow commands. Patient symptoms were suspected to be due to acute alcohol intoxication. Thus, the patient was given 40 mg of propofol intravenously. Following treatment, the patient recovered with less confusion and disorientation after approximately 10 min. After treatment with propofol twice more, he regained consciousness, was calm and cooperative, had no pain, and could obey instructions approximately 1 h and 40 min following the last treatment. Following this treatment, the patient was transferred to the inpatient ward and felt well.

Conclusions
It is paramount to correctly identify the underlying cause of emergence agitation in order to successfully manage patient symptoms, since treatment plans vary between different etiological causes. Emergence agitation may be due to acute alcohol intoxication after intraoperative use of alcohol.
Creating efficiencies in the extraction of data from randomized trials: a prospective evaluation of a machine learning and text mining tool
Authors: Gates Allison , Gates Michelle , Sim Shannon , Elliott Sarah A. , Pillay Jennifer , Hartling Lisa 
Published: August 2021

Abstract
Background
Machine learning tools that semi-automate data extraction may create efficiencies in systematic review production. We evaluated a machine learning and text mining tool’s ability to (a) automatically extract data elements from randomized trials, and (b) save time compared with manual extraction and verification.

Methods
For 75 randomized trials, we manually extracted and verified data for 21 data elements. We uploaded the randomized trials to an online machine learning and text mining tool, and quantified performance by evaluating its ability to identify the reporting of data elements (reported or not reported), and the relevance of the extracted sentences, fragments, and overall solutions. For each randomized trial, we measured the time to complete manual extraction and verification, and to review and amend the data extracted by the tool. We calculated the median (interquartile range [IQR]) time for manual and semi-automated data extraction, and overall time savings.

Results
The tool identified the reporting (reported or not reported) of data elements with median (IQR) 91% (75% to 99%) accuracy. Among the top five sentences for each data element at least one sentence was relevant in a median (IQR) 88% (83% to 99%) of cases. Among a median (IQR) 90% (86% to 97%) of relevant sentences, pertinent fragments had been highlighted by the tool; exact matches were unreliable (median (IQR) 52% [33% to 73%]). A median 48% of solutions were fully correct, but performance varied greatly across data elements (IQR 21% to 71%). Using ExaCT to assist the first reviewer resulted in a modest time savings compared with manual extraction by a single reviewer (17.9 vs. 21.6 h total extraction time across 75 randomized trials).

Conclusions
Using ExaCT to assist with data extraction resulted in modest gains in efficiency compared with manual extraction. The tool was reliable for identifying the reporting of most data elements. The tool’s ability to identify at least one relevant sentence and highlight pertinent fragments was generally good, but changes to sentence selection and/or highlighting were often required.

Protocol
https://doi.org/10.7939/DVN/RQPJKS
Do assisted living facilities that offer a dementia care program differ from those that do not? A population-level cross-sectional study in Ontario, Canada
Authors: Manis Derek R. , Rahim Ahmad , Poss Jeffrey W. , Bielska Iwona A. , Bronskill Susan E. , Tarride Jean-Éric , Abelson Julia , Costa Andrew P. 
Published: August 2021

Abstract
Background
Many residents of assisted living facilities live with dementia, but little is known about the characteristics of assisted living facilities that provide specialized care for older adults who live with dementia. In this study, we identify the characteristics of assisted living facilities that offer a dementia care program, compared to those that do not offer such a program.

Methods
We conducted a population-level cross-sectional study on all licensed assisted living facilities in Ontario, Canada in 2018 (n = 738). Facility-level characteristics (e.g., resident and suite capacities, etc.) and the provision of the other 12 provincially regulated care services (e.g., pharmacist and medical services, skin and wound care, etc.) attributed to assisted living facilities were examined. Multivariable Poisson regression with robust standard errors was used to model the characteristics of assisted living facilities associated with the provision of a dementia care program.

Results
There were 123 assisted living facilities that offered a dementia care program (16.7% versus 83.3% no dementia care). Nearly half of these facilities had a resident capacity exceeding 140 older adults (44.7% versus 21.6% no dementia care) and more than 115 suites (46.3% versus 20.8% no dementia care). All assisted living facilities that offered a dementia care program also offered nursing services, meals, assistance with bathing and hygiene, and administered medications. After adjustment for facility characteristics and other provincially regulated care services, the prevalence of a dementia care program was nearly three times greater in assisted living facilities that offered assistance with feeding (Prevalence Ratio [PR] 2.91, 95% Confidence Interval [CI] 1.98 to 4.29), and almost twice as great among assisted living facilities that offered medical services (PR 1.78, 95% CI 1.00 to 3.17), compared to those that did not.

Conclusions
A dementia care program was more prevalent in assisted living facilities that housed many older adults, had many suites, and offered at least five of the other 12 regulated care services. Our findings deepen the understanding of specialized care for dementia in assisted living facilities.