bluuebunny/crossref_metadata_2025_split huggingface dataset:
LncRNAs in domesticated animals: from dog to livestock species
Authors: Lagarrigue Sandrine , Lorthiois Matthias , Degalez Fabien , Gilot David , Derrien Thomas 
Published: November 2021

AbstractAnimal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
End-stage renal disease, calcification patterns and clinical outcomes after TAVI
Authors: Grundmann David , Linder Matthias , Goßling Alina , Voigtländer Lisa , Ludwig Sebastian , Waldschmidt Lara , Demal Till , Bhadra Oliver D. , Schäfer Andreas , Schirmer Johannes , Reichenspurner Hermann , Blankenberg Stefan , Westermann Dirk , Schofer Niklas , Conradi Lenard , Seiffert Moritz 
Published: November 2021

Abstract
Background
Patients with chronic hemodialysis due to end-stage renal disease (ESRD) or severely impaired kidney function (CKD) constitute a relevant share of patients undergoing trans-catheter aortic valve implantation (TAVI). However, data on specific challenges and outcomes remain limited.

Aim
We aimed to characterize this patient population, evaluate clinical results and assess the significance of calcification patterns.

Methods
This retrospective single-center analysis evaluated 2,712 TAVI procedures (2012–2019) according to baseline renal function: GFR < 30 ml/min/1.73m2 (CKD; n = 210), chronic hemodialysis (ESRD; n = 119) and control (CTRL; n = 2383). Valvular and vascular calcification patterns were assessed from contrast-enhanced multi-detector computed tomography. Outcomes were evaluated in accordance with the VARC-2 definitions.

Results
Operative risk was higher in ESRD and CKD vs. CTRL (STS-score 8.4% and 7.6% vs. 3.9%, p < 0.001) and patients with ESRD had more severe vascular calcifications (49.1% vs. 33.9% and 29.0%, p < 0.01). Immediate procedural results were similar but non-procedure-related major/life-threatening bleeding was higher in ESRD and CKD (5.0% and 5.3% vs. 1.6%, p < 0.01). 3-year survival was impaired in patients with ESRD and CKD (33.3% and 35.3% vs. 65.4%, p < 0.001). Multivariable analysis identified ESRD (HR 1.60), CKD (HR 1.79) and vascular calcifications (HR 1.29) as predictors for 3-year and vascular calcifications (HR 1.51) for 30-day mortality.

Conclusion
Patients with ESRD and CKD constitute a vulnerable patient group with extensive vascular calcifications. Immediate procedural results were largely unaffected by renal impairment, yielding TAVI a particularly valuable treatment option in these high-risk operative patients. Mid-term survival was determined by underlying renal disease, cardiovascular comorbidities, and vascular calcifications as a novel risk marker.

Graphical abstract
Assessment of renal glomerulosclerosis and thickness of the carotid intima-media complex as a means of age estimation in Western European bodies
Authors: Lehmann-Leo Carl Daniel , Ramsthaler Frank , Birngruber Christoph G. , Verhoff Marcel A. 
Published: November 2021

Abstract
Introduction
The estimation of age-at-death of unidentified cadavers is a central aspect of the identification process. With increasing age, the incidence of glomerulosclerosis and the thickness of the carotid wall have been observed to also increase. This correlation has been demonstrated in various international histological studies. The aim of our study was to assess whether these correlations also apply to a Western European population.

Methodology
In this retrospective observational study, kidney and common carotid artery samples from 216 cases autopsied at the Institute of Legal Medicine at the Justus-Liebig University in Giessen, Germany, were examined. Only cases with available tissue samples from both body sides were included. Exclusion criteria were poor sample quality and an age younger than 21 years. After histological processing, the tissue samples were assessed and digitally evaluated. Regression and classification analyses were used to investigate the correlation between age-at-death and intima-media thickness and age-at-death and the incidence of renal glomerular sclerosis.

Results
Of the 216 autopsy cases, 183 were included for evaluation. Analysis of the carotid artery segments showed a strong correlation (Pearson correlation coefficient r = 0.887) between the intima-media-complex thickness and chronological age. Classification of the glomerulosclerotic incidence showed a correlation of 37.7–43.1% with the predicted age group.

Discussion
Both the intima-media thickness and the proportion of sclerotic glomeruli can be used to estimate age in Western European cadavers. On the basis of these results, both methods are suited to supplement other already established methods for age-at-death estimation in the identification of an unknown cadaver.
Absence of hydrothermal oxygen isotope variations in host rocks supports magmatic origin of the giant Grängesberg iron oxide–apatite (IOA) deposit, Central Sweden
Authors: Weis Franz , Troll Valentin R. , Jonsson Erik , Högdahl Karin , Harris Chris , Sun Weian , Nilsson Katarina P. , Dahrén Börje 
Published: November 2021

AbstractThe origin of Kiruna-type iron oxide–apatite ores is controversial, and debate presently centres on a ‘magmatic’ versus a ‘hydrothermal’ mode of formation. To complement recent investigations on the Grängesberg iron oxide–apatite ore deposit in the northwestern part of the Palaeoproterozoic Bergslagen ore province in central Sweden, we investigated the oxygen isotope composition of the host rocks of this large iron oxide–apatite ore body. As the metavolcanic and metagranitoid country rocks around the Grängesberg ore body either pre-date or are coeval with ore formation, they would be expected to record an extensive isotopic imprint if the ore body had formed by large-scale hydrothermal processes involving an externally sourced fluid. A direct magmatic formation process, in turn, would have produced localized alteration only, concentrated on the immediate vicinity of the ore body. Here, we test these two hypotheses by assessing the oxygen isotope variations in the host rocks around the main Grängesberg iron oxide–apatite ore body. We analysed oxygen isotopes in quartz from metavolcanic (n = 17) and metagranitoid host rocks (n = 14) from the vicinity of the ore body, and up to 2 km distance along and across the strike of the ore body. Remarkably, we find no significant variation in δ18O values with distance from the ore body, or any deviations in country rock δ18O from common magmatic and/or regional values. Only two samples show shifts to values more negative than the common magmatic range, indicating highly localized hydrothermal overprint only. As a large-scale, low-temperature hydrothermal origin of the ore body through voluminous fluid percolation would be expected to have left a distinct imprint on the oxygen isotope values of the country rocks, our results are more consistent with an ortho-magmatic origin for the Grängesberg iron oxide–apatite ore.
The effect of posterior compression of the facet joints for initial stability and sagittal profile in the treatment of thoracolumbar fractures: a biomechanical study
Authors: Ruf Michael , Pitzen Tobias , Nennstiel Ivo , Volkheimer David , Drumm Jörg , Püschel Klaus , Wilke Hans-Joachim 
Published: November 2021

Abstract
Purpose
Surgical treatment of thoracolumbar A3-fractures usually comprises posterior fixation—in neutral position or distraction—potentially followed by subsequent anterior support. We hypothesized that additional posterior compression in circumferential stabilization may increase stability by locking the facets, and better restore the sagittal profile.

Methods
Burst fractures Type A3 were created in six fresh frozen cadaver spine segments (T12–L2). Testing was performed in a custom-made spinal loading simulator. Loads were applied as pure bending moments of ± 3.75 Nm in all six movement axes. We checked range of motion, neutral zone and Cobb’s angle over the injured/treated segment within the following conditions: Intact, fractured, instrumented in neutral alignment, instrumented in distraction, with cage left in posterior distraction, with cage with posterior compression.

Results
We found that both types of instrumentation with cage stabilized the segment compared to the fractured state in all motion planes. For flexion/extension and lateral bending, flexibility was decreased even compared to the intact state, however, not in axial rotation, being the most critical movement axis. Additional posterior compression in the presence of a cage significantly decreased flexibility in axial rotation, thus achieving stability comparable to the intact state even in this movement axis. In addition, posterior compression with cage significantly increased lordosis compared to the distracted state.

Conclusion
Among different surgical modifications tested, circumferential fixation with final posterior compression as the last step resulted in superior stability and improved sagittal alignment. Thus, posterior compression as the last step is recommended in these pathologies.
Outcomes of long-term nivolumab and subsequent chemotherapy in Japanese patients with head and neck cancer: 2-year follow-up from a multicenter real-world study
Authors: Yasumatsu Ryuji , Shimizu Yasushi , Hanai Nobuhiro , Kariya Shin , Yokota Tomoya , Fujii Takashi , Tsukahara Kiyoaki , Ando Mizuo , Hanyu Kenji , Ueda Tsutomu , Hirakawa Hitoshi , Takahashi Shunji , Ono Takeharu , Sano Daisuke , Yamauchi Moriyasu , Watanabe Akihito , Omori Koichi , Yamazaki Tomoko , Monden Nobuya , Kudo Naomi , Arai Makoto , Yonekura Syuji , Asakage Takahiro , Nekado Takahiro , Yamada Takayuki , Homma Akihiro 
Published: November 2021

Abstract
Background
We have previously reported the effectiveness and safety of nivolumab in patients with head and neck cancer (HNC) in real-world clinical practice in Japan. Here, we report long-term outcomes from this study in the overall population and subgroups stratified by subsequent chemotherapy.

Methods
In this multicenter, retrospective observational study, Japanese patients with recurrent or metastatic (R/M) HNC receiving nivolumab were followed up for 2 years. Effectiveness endpoints included overall survival (OS), OS rate, progression-free survival (PFS), and PFS rate. Safety endpoints included the incidence of immune-related adverse events (irAEs).

Results
Overall, 256 patients received a median of 6.0 doses (range: 1–52) of nivolumab over a median duration of 72.5 days (range: 1–736). Median OS was 9.5 months [95% confidence interval (CI) 8.2–12.0] and median PFS was 2.1 months (95% CI 1.8–2.7). A significant difference between 2-year survivors (n = 62) and non-2-year survivors was observed by median age (P = 0.0227) and ECOG PS (P = 0.0001). Of 95 patients who received subsequent chemotherapy, 54.7% received paclitaxel ± cetuximab. The median OS and PFS from the start of paclitaxel ± cetuximab were 6.9 months (95% CI 5.9–11.9) and 3.5 months (95% CI 2.3–5.5), respectively. IrAEs were reported in 17.2% of patients. Endocrine (7.0%) and lung (4.3%) disorders were the most common irAEs; kidney disorder (n = 1) was newly identified in this follow-up analysis.

Conclusions
Results demonstrated the long-term effectiveness of nivolumab and potential effectiveness of subsequent chemotherapy in patients with R/M HNC in the real-world setting. Safety was consistent with that over the 1-year follow-up.
Seasonal dynamics on nutritive value, chemical estimates and in vitro dry matter degradability of some woody species found in rangelands of South Africa
Authors: Ravhuhali Khuliso Emmanuel , Msiza Ntokozo Happy , Mudau Humbelani Silas 
Published: November 2021

AbstractUnlocking browse species in semi-arid regions can be a key to improving the livestock productivity. The research was conducted to assess the browse species variation in chemical composition and in vitro dry matter degradability as influenced by seasonal (summer and winter) changes. Leaves from ten randomly selected browsable trees from sixteen species (Vachellia karroo, Senegalia nigrescens, Vachellia nilotica, Balanites maughamii, Berchemia discolor, Berchemia zeyheri, Bridelia mollis, Combretum collinum, Combretum imberbe, Dalbergia melanoxylon, Dichrostachys cinerea, Grewia monticola, Grewia occidentalis, Melia azedarach, Ormocarpum kirkii and Ziziphus mucronata) were harvested before defoliation from the site in two seasons (summer and winter) and dried at room temperature and then ground for analysis. Two-way analysis was used to analyse chemical composition and in vitro ruminal dry matter degradability. Melia azedarach (343.7 g/kg DM) had the highest (p < 0.0001) CP content in summer. In winter, B. maughamii (210.3 g/kg DM) had the highest (p < 0.05) crude protein content. Combretum collinum (2.90 Mcal/kg) had a highest (p < 0.0001) metabolizable energy value in summer. Bridelia mollis, B. maughamii, B. discolor, C. collinum, C. imberbe, O. kirkii, S. nigrescens, V. nilotica, G. occidentalis and B. zeyheri had the same (p > 0.0001) dry matter degradability (DMD) 48 values across two seasons. In both seasons, most of these browse species have the potential to supplement low quality natural grasses because they go beyond the minimum requirement of protein and have coherent amounts of fibre concentration. There is a need to assess the bioactive compounds found in these browse species for the amelioration and also to maximize browsing of these species.
Modified Traces and the Nakayama Functor
Authors: Shibata Taiki , Shimizu Kenichi 
Published: November 2021

AbstractWe organize the modified trace theory with the use of the Nakayama functor of finite abelian categories. For a linear right exact functor Σ on a finite abelian category ${\mathscr{M}}$
M
, we introduce the notion of a Σ-twisted trace on the class $\text {Proj}({\mathscr{M}})$
Proj
(
M
)
of projective objects of ${\mathscr{M}}$
M
. In our framework, there is a one-to-one correspondence between the set of Σ-twisted traces on $\text {Proj}({\mathscr{M}})$
Proj
(
M
)
and the set of natural transformations from Σ to the Nakayama functor of ${\mathscr{M}}$
M
. Non-degeneracy and compatibility with the module structure (when ${\mathscr{M}}$
M
is a module category over a finite tensor category) of a Σ-twisted trace can be written down in terms of the corresponding natural transformation. As an application of this principal, we give existence and uniqueness criteria for modified traces. In particular, a unimodular pivotal finite tensor category admits a non-zero two-sided modified trace if and only if it is spherical. Also, a ribbon finite tensor category admits such a trace if and only if it is unimodular.
Reliability and efficiency of corneal thickness measurements using sterile donor tomography in the eye bank
Authors: Hamon Loïc , Quintin Adrien , Mäurer Stephanie , Weinstein Isabel , Langenbucher Achim , Seitz Berthold , Daas Loay 
Published: November 2021

Abstract
To evaluate the reliability and efficiency of sterile pachymetric measurements of donor corneas based on tomographic data using two different methods: a “manual” and a “(semi-)automated” method. Twenty-five (25) donor corneas (50%) stored in MI and 25 (50%) in MII were imaged 5 times consecutively using an anterior segment OCT (AS-OCT). The central corneal thickness (CCT) was measured both with the manual measurement tool of the AS-OCT (= CCTm) and with a MATLAB self-programmed software allowing (semi-)automated analysis (= CCTa). We analyzed the reliability of CCTm and CCTa using Cronbach´s alpha (α) and Wilcoxon signed-Rank Test.
Concerning CCTm, 68 measurements (54.4%) in MI and 46 (36.8%) in MII presented distortions in the imaged 3D-volumes and were discarded. Concerning CCTa, 5 (4%) in MI and 1 (0.8%) in MII were not analyzable. The mean (± SD) CCTm was 1129 ± 6.8 in MI and 820 ± 5.1 µm in MII. The mean CCTa was 1149 ± 2.7 and 811 ± 2.4 µm, respectively. Both methods showed a high reliability with a Cronbach´s α for CCTm of 1.0 (MI/MII) and for CCTa of 0.99 (MI) and 1.0 (MII). Nevertheless, the mean SD of the 5 measurements was significantly higher for CCTm compared to CCTa in MI (p = 0.03), but not in MII (p = 0.92).
Sterile donor tomography proves to be highly reliable for assessment of CCT with both methods. However, due to frequent distortions regarding the manual method, the (semi-)automated method is more efficient and should be preferred.
Introducing Statistical Inference: Design of a Theoretically and Empirically Based Learning Trajectory
Authors: van Dijke-Droogers Marianne , Drijvers Paul , Bakker Arthur 
Published: November 2021

AbstractThis paper comprises the results of a design study that aims at developing a theoretically and empirically based learning trajectory on statistical inference for 9th-grade students. Based on theories of informal statistical inference, an 8-step learning trajectory was designed. The trajectory consisted of two similar four step sequences: (1) experimenting with a physical black box, (2) visualizing distributions, (3) examining sampling distributions using simulation software, and (4) interpreting sampling distributions to make inferences in real -life contexts. Sequence I included only categorical data and Sequence II regarded numerical data. The learning trajectory was implemented in an intervention among 267 students. To examine the effects of the trajectory on students’ understanding of statistical inference, we analyzed their posttest results after the intervention. To investigate how the stepwise trajectory fostered the learning process, students’ worksheets during each learning step were analyzed. The posttest results showed that students who followed the learning trajectory scored significantly higher on statistical inference and on concepts related to each step than students of a comparison group (n = 217) who followed the regular curriculum. Worksheet analysis demonstrated that the 8-step trajectory was beneficial to students’ learning processes. We conclude that ideas of repeated sampling with a black box and statistical modeling seem fruitful for introducing statistical inference. Both ideas invite more advanced follow-up activities, such as hypothesis testing and comparing groups. This suggests that statistics curricula with a descriptive focus can be transformed to a more inferential focus, to anticipate on subsequent steps in students’ statistics education.
Genetic Testing in Patients with Neurodevelopmental Disorders: Experience of 511 Patients at Cincinnati Children's Hospital Medical Center
Authors: Du Xiaoli , Glass Jennifer Elaine , Balow Stephanie , Dyer Lisa M. , Rathbun Pamela A. , Guan Qiaoning , Liu Jie , Wu Yaning , Dawson D. Brian , Walters-Sen Lauren , Smolarek Teresa A. , Zhang Wenying 
Published: November 2021

AbstractOur institution developed and continuously improved a Neurodevelopmental Reflex (NDR) algorithm to help physicians with genetic test ordering for neurodevelopmental disorders (NDDs). To assess its performance, we performed a retrospective study of 511 patients tested through NDR from 2018 to 2019. SNP Microarray identified pathogenic/likely pathogenic copy number variations in 27/511 cases (5.28%). Among the 484 patients tested for Fragile X FMR1 CGG repeats, a diagnosis (0.20%) was established for one male mosaic for a full mutation, a premutation, and a one-CGG allele. Within the 101 normocephalic female patients tested for MECP2, two patients were found to carry pathogenic variants (1.98%). This retrospective study suggested the NDR algorithm effectively established diagnoses for patients with NDDs with a yield of 5.87%.
Performance of a machine-learning algorithm to predict hypotension in mechanically ventilated patients with COVID-19 admitted to the intensive care unit: a cohort study
Authors: van der Ven Ward H. , Terwindt Lotte E. , Risvanoglu Nurseda , Ie Evy L. K. , Wijnberge Marije , Veelo Denise P. , Geerts Bart F. , Vlaar Alexander P. J. , van der Ster Björn J. P. 
Published: November 2021

AbstractThe Hypotension Prediction Index (HPI) is a commercially available machine-learning algorithm that provides warnings for impending hypotension, based on real-time arterial waveform analysis. The HPI was developed with arterial waveform data of surgical and intensive care unit (ICU) patients, but has never been externally validated in the latter group. In this study, we evaluated diagnostic ability of the HPI with invasively collected arterial blood pressure data in 41 patients with COVID-19 admitted to the ICU for mechanical ventilation. Predictive ability was evaluated at HPI thresholds from 0 to 100, at incremental intervals of 5. After exceeding the studied threshold, the next 20 min were screened for positive (mean arterial pressure (MAP) < 65 mmHg for at least 1 min) or negative (absence of MAP < 65 mmHg for at least 1 min) events. Subsequently, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and time to event were determined for every threshold. Almost all patients (93%) experienced at least one hypotensive event. Median number of events was 21 [7–54] and time spent in hypotension was 114 min [20–303]. The optimal threshold was 90, with a sensitivity of 0.91 (95% confidence interval 0.81–0.98), specificity of 0.87 (0.81–0.92), PPV of 0.69 (0.61–0.77), NPV of 0.99 (0.97–1.00), and median time to event of 3.93 min (3.72–4.15). Discrimination ability of the HPI was excellent, with an area under the curve of 0.95 (0.93–0.97). This validation study shows that the HPI correctly predicts hypotension in mechanically ventilated COVID-19 patients in the ICU, and provides a basis for future studies to assess whether hypotension can be reduced in ICU patients using this algorithm.