bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of a Very Short-Stay Post-Emergency Geriatric Unit on Early Readmissions
Authors: Moyet Julien , Lesourd Baptiste , Bachelet Félix , Delattre Orianne , Domisse Laure , Hannat Sanaa , Defouilloy Christian , Bloch Frédéric 
Published: October 2022

Background and Objectives:
In 2017, our French 1671-bed university hospital opened a 12-bed unit for very short stays, post-emergency (unit of transitory admission in geriatric [UTAG] area), dedicated to frail patients older than 75 years requiring short-term care. We sought to investigate whether this new organization's shortened length of stay (LOS) was associated or not with a higher rate of readmission.

Methods:
We conducted a retrospective descriptive study based on the daily activity of the UTAG over 6 months including all patients consecutively hospitalized in the unit via the computerized medical file of the hospital. The data collected included the Rockwood score, the primary diagnoses, the LOS and any 1-month readmission.

Results:
From August 2019 to January 2020, 646 older adult patients were hospitalized in the UTAG. Two-thirds of the hospitalized patients were women; the mean age of this population was 86.7 ± 6.2 years. The main causes of hospitalization were infectious pathologies (19.8%), falls and their consequences (17.3%), and cardiac pathologies (17.2%). The mean LOS was of 2.7 ± 2.0. Seventy readmissions were observed in the month after discharge. One-month readmissions were more frequent when patients had presented with acute heart failure and among nursing home residents.

Conclusion:
The creation of the UTAG reduced LOS and so contributed to decreased iatrogenic disabilities without putting patients at increased risk of readmission. The development of cardiac and geriatric dedicated outpatient pathways and a community-based geriatric mobile team intervening in nursing homes could optimize the care of frail older adult patients and avoid readmissions.
Comparative Study of the Incidence of Port Site Infection in Disposable Ports and Reprocessed Disposable Ports in Laparoscopic Cholecystectomy
Authors: Jokar Mozhgan , Larti Negin , Zarei Mohammadreza , Melali Hamid , Zabihirad Jaber , Maraki Fatemeh , Jazini Dorcheh Saeed , Kelidari Behrooz 
Published: October 2022

Introduction:
Port site infection (PSI) is a rare complication of laparoscopic surgery that can reduce the benefits of this minimally invasive surgery and increase postoperative complications. As a variety of disposable ports (single-use ports) and reprocessed ports are used in laparoscopic surgeries, this study was conducted to compare the incidence of PSI in disposable ports and reprocessed disposable ports in laparoscopic cholecystectomy (LC).

Materials and Methods:
In this prospective cohort study, 473 patients were studied. Two hundred fifteen and two hundred fifty eight were in the disposable port group and reprocessed disposable port group, respectively. The demographic characteristics and incidence of superficial and deep infection were evaluated using the researcher-made checklist of infection assessment standards at intervals of 3 to 5 and 5 to 14 days following LC using call and physical examination on day 14. Data analysis was performed using descriptive statistics and statistical tests in SPSS software.

Results:
The incidence of PSI, 3 to 5 and 5 to 14 days after surgery in the reprocessed disposable port group was significantly higher than that in the disposable ports group. In both groups, all PSI accrued in the epigastric port area (where the gallbladder was removed) (P< 0.05).

Conclusion:
On the basis of the results, our study suggests using disposable ports instead, and in the case of using reprocessed disposable ports in LC, upgrading of disinfection and sterilization techniques is necessary.
Gastric Emptying is Accelerated in Patients With Gastric Tube Reconstruction Following Laparoscopic Proximal Gastrectomy
Authors: Toyomasu Yoshitaka , Mochiki Erito , Ito Tetsuya , Ishiguro Toru , Suzuki Okihide , Kumagai Youichi , Ishibashi Keiichiro , Saeki Hiroshi , Shirabe Ken , Ishida Hideyuki 
Published: October 2022

Background:
Laparoscopic proximal gastrectomy (LPG) is an attractive option for the treatment of early gastric cancer in the upper third of the stomach. No optimal method of reconstruction after LPG has been established because of problems associated with postoperative reflux. Gastric tube reconstruction, a type of esophagogastrostomy, is a simple procedure, but it is associated with a high frequency of reflux esophagitis (RE). We investigated the relationship between RE and gastric emptying, along with nutritional parameters.

Subjects and Methods:
We compared gastric emptying in patients who had undergone curative LPG with gastric tube reconstruction for gastric cancer with that of patients after total gastrectomy (TG), distal gastrectomy (DG) and of healthy volunteers and patients after DG. The LPG group was divided into an RE LPG-RE (+) group and a non-reflux esophagitis (non-RE) an LPG-RE (−) group, and we compared gastric emptying and indices of nutrition, such as body weight and laboratory findings, between those among LPG-RE (+), LPG-RE (−), and TG groups.

Results:
The time lag between ingestion and peak 13CO2 expiration (T lag) in the healthy volunteer group was significantly shorter in the LPG group longer than those in the healthy volunteer LPG group and TG group. The T lag was significantly shorter in the RE LPG-RE (+) group than in the non-RE LPG-RE (−) group. The percentage change in body weight percentage in the non-RE LPG-RE (−) group was significantly larger than that in the RE LPG-RE (+) group at 12 months after surgery. Both the serum albumin and hemoglobin levels in the non-RE LPG-RE (−) tended to be preserved compared with those in the RE LPG-RE (+) group and TG group.

Conclusions:
Gastric emptying was accelerated after LPG, and was associated with RE. Our data suggest that RE could be associated with body weight loss after LPG.
On the eigenstructure of rotations and poses: commonalities and peculiarities
Authors: D’Eleuterio Gabriele M. T. , Barfoot Timothy D. 
Published: October 2022

Locating vehicles, targets and objects in three-dimensional space is key to many fields of science and engineering such as robotics, aerospace, computer vision and graphics. Rotations and poses (position plus orientation) of bodies can be expressed in a variety of ways. Rotation matrices constitute one of the classic matrix Lie groups, the special orthogonal group—SO(3). Poses can likewise be represented by matrices. One such representation is embodied in a 4 × 4 matrix establishing another famous matrix Lie group, the special Euclidean group—SE(3). An alternative representation of pose uses 6 × 6 matrices and is referred to as the group of pose adjoints—Ad(SE(3)). The eigenstructures of these representations reveal much about them from Euler’s theorem for rotations to the Mozzi–Chasles theorem for the general displacement of a rigid body. While the eigenstructure ofSO(3)has been extensively studied, those ofSE(3)andAd(SE(3))have hardly received the same scrutiny yet their structure is much richer. Motivated by their importance in kinematics and dynamics, we provide here a complete characterization of rotations and poses in terms of the eigenstructure of their matrix Lie group representations. An eigendecomposition of pose matrices reveals that they can be cast into a form similar to that of rotations although the structure of the former can vary depending on the nature of the pose involved. In particular, the pose matrices ofSE(3)andAd(SE(3))cannot generally be diagonalized as can rotation matrices but they of course do yield to a Jordan normal form, from which we can identify a principal-axis pose in much the same manner that we can a principal-axis rotation. We also address the minimal polynomials for poses and derive a novel expression for the Jacobian inAd(SE(3)). Finally, we argue that the true counterpart toSO(3)for poses is notSE(3)butAd(SE(3)).
Supplementation of AQUATURM® (Water soluble turmeric extract) prior to and following heavy eccentric exercise alleviates symptoms of Delayed onset muscle soreness (DOMS)
Authors: Tamoli Sanjay , Mundhe Narendra , Pawar Vinay , Birari Sandip 
Published: October 2022

AbstractBackgroundCurcumin, the most active component in turmeric helps attenuate DOMS.ObjectivesA clinical study was conducted to evaluate efficacy and safety of AQUATURM® in subjects with Delayed Onset Muscle Soreness (DOMS).MethodsTwenty healthy men in each of the two subsets completed the study. Subjects were assigned as per a computer-generated randomization list. In subset-I, subjects were asked to take given product in a dose of 1 capsule (250 mg) for 2 days. In subset-II, subjects were asked to take given product in a dose of 1 capsule (250mg) for 5 days. In subset-I, eccentric exercise was performed at hour 6. In subset-II eccentric exercise was performed at day 2.5. The outcome measures were muscle pain, tenderness, swelling, jump performance, muscle inflammatory markers, rescue medication and adverse events. These outcome measures were evaluated at 0 hour, at 6 hours (immediately after exercise), at 24 hours and at 48 hours in subset-I, and at day 1, day 2.5 baseline (immediately after exercise), at 24 hours from baseline and at 48 hours from baseline in subset-II.ResultsA significant reduction in muscle pain, tenderness and swelling post eccentric exercise was observed in AQUATURM® Capsule group compared to placebo group in both the subsets of the study. Additionally, when compared to the placebo group, the AQUATURM® group showed a statistically significant increase in post exercise average single-leg vertical squat jump. AQUATURM® Capsule was well tolerated by the subjects.ConclusionSupplementation of AQUATURM® Capsule prior to and following heavy eccentric exercise in healthy men resulted in relieving muscle pain, tenderness and swelling from DOMS.
High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptideaspp.)
Authors: Höök L. , Näsvall K. , Vila R. , Wiklund C. , Backström N. 
Published: October 2022

AbstractKaryotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genusLeptideahas an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between theLeptideaspecies, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling.
Genome-wide RNA binding analysis ofC9orf72poly(PR) dipeptides
Authors: Balendra Rubika , de los Mozos Igor Ruiz , Glaria Idoia , Milioto Carmelo , Odeh Hana M , Wilson Katherine M , Ule Agnieszka M , Hallegger Martina , Masino Laura , Martin Stephen , Patani Rickie , Shorter James , Ule Jernej , Isaacs Adrian M 
Published: October 2022

AbstractAn intronic GGGGCC repeat expansion inC9orf72is a common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. The repeats are transcribed in both sense and antisense directions to generate distinct dipeptide repeat proteins, of which poly(GA), poly(GR) and poly(PR) have been implicated in contributing to neurodegeneration. Poly(PR) binding to RNA may contribute to toxicity, but analysis of poly(PR)-RNA binding on a genome-wide scale has not yet been carried out. We therefore performed crosslinking and immunoprecipitation (CLIP) analysis in human cells to identify the RNA binding sites of poly(PR). We found that poly(PR) binds to nearly 600 RNAs, with the sequence GAAGA enriched at the binding sites.In vitroexperiments showed that polyGAAGA RNA binds poly(PR) with higher affinity than control RNA and induces phase-separation of poly(PR) into condensates. These data indicate that poly(PR) preferentially binds to polyGAAGA-containing RNAs, which may have physiological consequences.
Barcoded overexpression screens in gut Bacteroidales identify genes with new roles in carbon utilization and stress resistance
Authors: Huang Yolanda Y. , Price Morgan N. , Hung Allison , Gal-Oz Omree , Ho Davian , Carion Héloïse , Deutschbauer Adam M. , Arkin Adam P. 
Published: October 2022

AbstractA mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to- phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed inEscherichia coliand assayed in a small number of conditions. To address these challenges, we developed Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed inBacteroides thetaiotaomicron. From hundreds of experiments, we identified new functions and novel phenotypes for 29 genes involved in carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a D- glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assay types.
Emergent neural dynamics and geometry for generalization in a transitive inference task
Authors: Kay Kenneth , Biderman Natalie , Khajeh Ramin , Beiran Manuel , Cueva Christopher J. , Shohamy Daphna , Jensen Greg , Wei Xue-Xin , Ferrera Vincent P. , Abbott L.F. 
Published: October 2022

AbstractRelational cognition — the ability to infer relationships that generalize to novel combinations of objects — is fundamental to human and animal intelligence. Despite this importance, it remains unclear how relational cognition is implemented in the brain due in part to a lack of hypotheses and predictions at the levels of collective neural activity and behavior. Here we discovered, analyzed, and experimentally tested neural networks (NNs) that perform transitive inference (TI), a classic relational task (if A > B and B > C, then A > C). We found NNs that (i) generalized perfectly, despite lacking overt transitive structure prior to training, (ii) generalized when the task required working memory (WM), a capacity thought essential to inference in the brain, (iii) emergently expressed behaviors long observed in living subjects, in addition to a novel order-dependent behavior, and (iv) adopted different task solutions yielding alternative behavioral and neural predictions. Further, in a large-scale experiment, we found that human subjects performing WM-based TI showed behavior inconsistent with a class of NNs expressing an intuitive task solution. These findings provide neural insights into a classical relational ability, with wider implications for how the brain realizes relational cognition.
The identity ofArgyria lacteella(Fabricius, 1794) (Lepidoptera, Pyraloidea, Crambinae), synonyms, and related species using morphology and DNA capture in type specimens
Authors: Landry Bernard , Bilat Julia , Hayden James , Solis M. Alma , Lees David C. , Alvarez Nadir , Léger Théo , Gauthier Jérémy 
Published: October 2022

AbstractRecent developments in museomics enable genetic information to be recovered from previously unusable collection specimens and thus to answer complex taxonomic questions. Here we apply museomics to a taxonomic problem involving several species ofArgyriaHübner (Pyraloidea, Crambinae), with previously unrecognized morphological variation. By analysing the DNA barcode (COI-5P) in numerous specimens, we aimed to reconstruct phylogenetic relationships between species, to provide better evidence for synonymies, and to circumscribe their geographical distribution. Using an innovative DNA hybridization capture protocol, we partially recovered the DNA barcode of the lectotype ofArgyria lacteella(Fabricius, 1794) for comparison with the 229 DNA barcode sequences ofArgyriaspecimens available in the Barcode of Life Datasystems, and this firmly establishes the identity of the species. The same protocol was used for the following type specimens: theArgyria abronalis(Walker, 1859) holotype, thus confirming the synonymy of this name withA. lacteella, the holotype ofA. lusella(Zeller, 1863),rev. syn., the holotype ofA. multifactaDyar, 1914,syn. n., newly synonymized withA. lacteella, and a specimen ofArgyria diplomochalisDyar, 1913, collected in 1992. A complementary sampling composed of nine specimens ofA. lacteella, A. diplomochalis, A. centrifugensDyar, 1914 andA. gonogrammaDyar, 1915, from North to South America, were integrated using classical COI amplification and Sanger sequencing.Argyria gonogrammaDyar, described from Bermuda, is the name to be applied to the more widespread North American species formerly identified asA. lacteella. Following morphological study of its holotype,Argyria vestalisButler, 1878,syn. n. is also synonymized withA. lacteella. The nameA. pusillalisHübner, 1818, is considered anomen dubiumassociated withA. gonogramma. The adult morphology is diagnosed and illustrated, and distributions are plotted forA. lacteella, A. diplomochalis, A. centrifugens, andA. gonogrammabased on slightly more than 800 specimens. For the first time, DNA barcode sequences are provided for the AntilleanA. diplomochalis. Our work highlights the efficiency of the DNA hybrid capture enrichment method to retrieve DNA barcodes from 18th and 19th century type specimens in order to solve taxonomic issues in Lepidoptera.
Pytometry: Flow and mass cytometry analytics in Python
Authors: Büttner Maren , Hempel Felix , Ryborz Thomas , Theis Fabian J. , Schultze Joachim L. 
Published: October 2022

AbstractFlow and mass cytometry data are commonly analyzed via manual gating strategies which requires prior knowledge, expertise and time. With increasingly complex experiments with many parameters and samples, traditional manual flow and mass cytometry data analysis becomes cumbersome if not inefficient. At the same time, computational tools developed for the analysis of single-cell RNA-sequencing data have made single cell genomics analysis highly efficient, yet they are mostly inaccessible for the analysis of flow and mass cytometry data due to different data formats, noise assumptions and scales. To bring the advantages of both fields together, we developed Pytometry as an extension to the popular scanpy framework for the analysis of flow and mass cytometry data. We showcase a standard analysis workflow on healthy human bone marrow data, illustrating the applicability of tools developed for the larger feature space of single cell genomics data. Pytometry combines joint analysis of multiple samples and advanced computational applications, ranging from automated pre-processing, cell type annotation and disease classification.
Expanding the synthetic biology toolbox with a library of constitutive and repressible promoters
Authors: Yang Eric J.Y. , Nemhauser Jennifer L. 
Published: October 2022

Structured AbstractBackgroundTo support the increasingly complex circuits needed for plant synthetic biology applications, additional constitutive promoters are essential. Reusing promoter parts can lead to difficulty in cloning, increased heterogeneity between transformants, transgene silencing and trait instability. Moreover, the utility of such promoters could be increased by introducing target sequences not found elsewhere in theArabidopsis thalianagenome and well-suited for Cas9-associated guide RNAs (gRNAs).MethodsWe have developed a pipeline to identify genes that have stable expression across a wide range ofArabidopsistissues at different developmental stages, and have identified a number of promoters that are well expressed in both transient (Nicotiana benthamiana) and stable (Arabidopsis) transformation assays. We have also introduced two genome-orthogonal gRNA target-sites in a subset of the screened promoters, converting them into NOR logic gates.ResultsOf twenty-two promoters identified in our bioinformatic screen, sixteen drove detectable reporter expression inN. benthamiana. Only three of these promoters were able to produce visible expression of the RUBY reporter inArabidopsisdespite producing RUBY mRNA that could be readily detected by qPCR. We then modified six of these promoters to be repressible, and five of which functioned as NOR gatesConclusionsOne of the major bottlenecks for the ambitious engineering projects currently under development in plants is the lack of well-characterized constitutive promoters. The work here begins to fill this gap. It can also form the basis of constructing more complex information processing circuits in the future.