bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying fish and estimating abundance and swim velocities of migrating Pacific salmon using adaptive resolution imaging sonar in mobile surveys
Authors: Xie Yunbo , Hornsby Rachael L , Hanot William H , Bartel-Sawatzky Michael , Nelitz Jacqueline L 
Published: July 2024

Abstract
Mobile acoustic sounding is an effective survey method for fish abundance residing or migrating in large riverine basins and marine areas. A long-standing challenge in acoustic fish surveys with conventional sonar is the uncertainty in identifying fish targets from acquired echo data. Identification errors of fish targets can significantly bias estimates of fish abundances and negatively impact the management of fisheries. In contrast to conventional sonar, adaptive resolution imaging sonar (ARIS), if deployed properly with appropriate settings, can yield high-quality images of fish targets. ARIS images acquired with adequate frame rates can form video recordings to allow for confident identification of fish targets from recorded morphological features, sizes, direction of movements, and speeds. In this paper, we present an approach of using ARIS sonar for mobile surveys of fish passage in a riverine environment. Applications of this approach are demonstrated for its practical values with results from an ARIS-based mobile survey of upstream migrating salmon at an acoustically challenging fish-counting site on the lower Fraser River in British Columbia, Canada.
Democracy and defections
Authors: Khosla Madhav , Vaishnav Milan 
Published: July 2024

Abstract
Within comparative constitutional law, there is an emerging consensus that political fragmentation has weakened political parties and hindered the functioning of legislative bodies. This article examines legal efforts to curb fragmentation in parliamentary systems by prohibiting floor crossing, or “defections”—a constitutional approach that concentrates power within party leaders. It conducts a detailed case study of India, exploring what is arguably the most extensive experiment in anti-defection law and its impact on accountability and representation. The article goes on to analyze similar laws in Israel and South Africa, highlighting the challenges of self-regulation. After evaluating the limitations of narrow anti-defection laws—such as the one in Pakistan—it proposes that the drawbacks of legislating party unity through formal defection regulation may prompt a reconsideration not only of legislatures but also political parties and political polarization. While some scholars have viewed attempts to stem fragmentation as a solution for limiting polarization, this article suggests the opposite: sharpening polarization, when coupled with norm-based internal party controls, may well tame the excesses of fragmentation, especially in non-programmatic multiparty systems. Although there are difficult tradeoffs here, as polarization can have independent (adverse) effects, the broader lessons of anti-defection laws deserve to be reckoned with. Ultimately, however, what the widespread adoption of anti-defection laws might primarily reveal is the nature of our faith—or lack thereof—in the promise of a certain form of parliamentary politics.
Long-term accuracy of numerical approximations of SPDEs with the stochastic Navier–Stokes equations as a paradigm
Authors: Glatt-Holtz Nathan E , Mondaini Cecilia F 
Published: July 2024

Abstract
This work introduces a general framework for establishing the long time accuracy for approximations of Markovian dynamical systems on separable Banach spaces. Our results illuminate the role that a certain uniformity in Wasserstein contraction rates for the approximating dynamics bears on long time accuracy estimates. In particular, our approach yields weak consistency bounds on ${\mathbb{R}}^{+}$ while providing a means to sidestepping a commonly occurring situation where certain higher order moment bounds are unavailable for the approximating dynamics. Additionally, to facilitate the analytical core of our approach, we develop a refinement of certain ‘weak Harris theorems’. This extension expands the scope of applicability of such Wasserstein contraction estimates to a variety of interesting stochastic partial differential equation examples involving weaker dissipation or stronger nonlinearity than would be covered by the existing literature. As a guiding and paradigmatic example, we apply our formalism to the stochastic 2D Navier–Stokes equations and to a semi-implicit in time and spectral Galerkin in space numerical approximation of this system. In the case of a numerical approximation, we establish quantitative estimates on the approximation of invariant measures as well as prove weak consistency on ${\mathbb{R}}^{+}$. To develop these numerical analysis results, we provide a refinement of $L^{2}_{x}$ accuracy bounds in comparison to the existing literature, which are results of independent interest.
dg-Hecke Duality and Tensor Products
Authors: Schneider Peter , Sorensen Claus 
Published: July 2024

Abstract
We continue our study of the monoidal category $D(G)$ begun in [ 12]. At the level of cohomology we transfer the duality functor $R\underline{\operatorname{Hom}}(-,k)$ to the derived category of dg-modules $D(H_{U}^{\bullet })$. In the process we develop a more general and streamlined approach to the anti-involution $\mathscr J$ from [ 8]. We also verify that the tensor product on $D(G)$ corresponds to an operadic tensor product on the dg-side (cf [ 5]). This uses a result of Schnürer on dg-categories with a model structure.
Quantum Lefschetz Without Curves
Authors: Oh Jeongseok , Thomas Richard P 
Published: July 2024

Abstract
Given one quasi-smooth derived space cut out of another by a section of a 2-term complex of bundles, we give two formulae for its virtual cycle. They are modelled on the the $p$-fields construction of Chang–Li and the Quantum Lefschetz principle, and recover these when applied to moduli spaces of (stable or quasi-) maps. When the complex is a single bundle we recover the results of Kim–Kresch–Pantev.
Air monitoring by nanopore sequencing
Authors: Reska Tim , Pozdniakova Sofya , Borràs Sílvia , Perlas Albert , Sauerborn Ela , Cañas Lídia , Schloter Michael , Rodó Xavier , Wang Yuanyuan , Winkler Barbro , Schnitzler Jörg-Peter , Urban Lara 
Published: July 2024

AbstractWhile the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome’s composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city’s boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.
Effect of digital tools to promote hospital quality and safety on adverse events after discharge
Authors: Vasudevan Anant , Plombon Savanna , Piniella Nicholas , Garber Alison , Malik Maria , O’Fallon Erin , Goyal Abhishek , Gershanik Esteban , Kumar Vivek , Fiskio Julie , Yoon Cathy , Lipsitz Stuart R , Schnipper Jeffrey L , Dalal Anuj K 
Published: July 2024

Abstract

Objectives
Post-discharge adverse events (AEs) are common and heralded by new and worsening symptoms (NWS). We evaluated the effect of electronic health record (EHR)-integrated digital tools designed to promote quality and safety in hospitalized patients on NWS and AEs after discharge.

Materials and Methods
Adult general medicine patients at a community hospital were enrolled. We implemented a dashboard which clinicians used to assess safety risks during interdisciplinary rounds. Post-implementation patients were randomized to complete a discharge checklist whose responses were incorporated into the dashboard. Outcomes were assessed using EHR review and 30-day call data adjudicated by 2 clinicians and analyzed using Poisson regression. We conducted comparisons of each exposure on post-discharge outcomes and used selected variables and NWS as independent predictors to model post-discharge AEs using multivariable logistic regression.

Results
A total of 260 patients (122 pre, 71 post [dashboard], 67 post [dashboard plus discharge checklist]) enrolled. The adjusted incidence rate ratios (aIRR) for NWS and AEs were unchanged in the post- compared to pre-implementation period. For patient-reported NWS, aIRR was non-significantly higher for dashboard plus discharge checklist compared to dashboard participants (1.23 [0.97,1.56], P = .08). For post-implementation patients with an AE, aIRR for duration of injury (&gt;1 week) was significantly lower for dashboard plus discharge checklist compared to dashboard participants (0 [0,0.53], P &lt; .01). In multivariable models, certain patient-reported NWS were associated with AEs (3.76 [1.89,7.82], P &lt; .01).

Discussion
While significant reductions in post-discharge AEs were not observed, checklist participants experiencing a post-discharge AE were more likely to report NWS and had a shorter duration of injury.

Conclusion
Interventions designed to prompt patients to report NWS may facilitate earlier detection of AEs after discharge.

ClinicalTrials.gov
NCT05232656
Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay
Authors: Min Byeng R , Wang Wei , Pitta Dipti W , Indugu Nagaraju , Patra Amlan K , Wang Hong He , Abrahamsen Frank , Hilaire Mariline , Puchala Ryszard 
Published: July 2024

Abstract
Understanding ruminal microbiota and diet–host breed interactions under forage feeding conditions is essential for optimizing rumen fermentation and improving feed efficiency in small ruminants. This study aimed to investigate the effects of different ratios of condensed tannin-rich Sericea lespedeza (SL; Lespedeza cuneata) in the diets on changes and interactions of ruminal microbiota and host species (i.e., sheep and goats). Katahdin sheep (n = 12) and Alpine goats (n = 12) at approximately 10 to 12 mo of age were blocked by body weight (BW = 30.3 and 25.5 kg, respectively) and randomly assigned to one of the 3 treatments. Diets contained 75% coarsely ground forage and 25% concentrate. The forages were 1) 100% alfalfa hay (AL), 2) 100% SL, and 3) 50% AL + 50% SL (ASL). In the present study, the diversity and composition of ruminal microbiota differed between sheep and goats fed similar diets. Based on the taxonomic analysis, there was a distinct clustering pattern (P &lt; 0.05) for sheep by diets, but such a pattern was not observed for goats (P &gt; 0.1). The most predominant phyla were Firmicutes, Bacteroidetes, Ascomycota, and methanogen species of Methanobrevibactor sp. in the rumen of sheep and goats, regardless of diets. The Bacteroidetes and Ascomycota were enriched in sheep fed AL and ASL. In contrast, these microbial phyla were enhanced in goats fed tannin-rich SL diets, with the diet-by-host species interaction (P &lt; 0.02) for the Bacteroidetes phylum. Sheep rumen fluid samples showed a higher degree of variability in microbial community composition compared to goat rumen fluid samples. The relative proportion of the Aspergillus fungi population was reduced to 90.7% in the SL group compared with the AL group, regardless of host species. The antimicrobial activity of tannins and greater sensitivities of selected microbiota species to these tannin compounds during SL feeding in sheep and goats perhaps caused this difference. The results from this study suggest that differences in the microbiota were associated with differences in diets and host species. Therefore, this study provides a better understanding of ruminal microbiota and diet–host species interactions under various tannin-rich diets, which could advance consolidative information on rumen microbiome community diversity changes and may improve sheep and goat production.
Sex-specific phosphorus (P)-use and -acquisition in dioecious Populus euphratica under different soil moisture levels
Authors: Si Shengwei , He Yue , Li Zongpei , Xia Zhichao 
Published: July 2024

Abstract
Dioecious plants show sexual dimorphism in their phosphorus (P) availability responses. However, the understanding of sex-specific strategies for P utilization and acquisition under varying soil moisture levels remains unclear. Here, we assessed a range of root functional traits, soil P properties, total foliar P concentration ([P]) and leaf chemical P fractions—inorganic P ([Pi]), metabolite P ([PM]), lipid P ([PL]), nucleic acid P ([PN]) and residual P ([PR])—as well as other leaf functional traits in female and male trees under different soil moisture levels (25% for high and 7% for low). Our results showed that females had larger specific root length under well-watered conditions, resulting in greater root foraging capacity. This led to a 36.3% decrease in soil active [Pi] in the rhizosphere and a 66.9 % increase in total foliar [P], along with all five foliar chemical P fractions ([Pi], [PM], [PL], [PN] and [PR]) compared with males. However, males exhibited significantly higher photosynthetic P utilization efficiency than females. Especially under low soil moisture levels, males exhibited a significant reduction in soil active organic P, coupled with a large increase in the exudation of soil phosphatases and carboxylates. Furthermore, the proportion of [PM] in total foliar [P] was 42.0% higher in males than in females. Mantel and Spearman correlation analyses revealed distinct coordination and trade-offs between foliar P fraction allocation and below-ground P acquisition strategies between the two sexes. Leveraging these sex-specific strategies could enhance the resilience of dioecious populations in forest plantations facing climate-induced variability.
Rohingya women as refugees: Examining displacement, refugeehood and ‘bare life’
Authors: Paul Samanwita , Butola Balbir Singh 
Published: July 2024

Abstract
Based on Agamben’s assertions (1998) refugees are often compared to ‘bare life’ (homo sacer) without any political agency. They are considered to be outside the purview of national or international legal and yet at its mercy for survival. For refugee women, this stripping of their autonomy stereotypes them as reproductive vessels in need of chivalrous protection within the larger refugee discourse. Policy projects frequently regard them as ‘vulnerable populations’ in need of assistance. Given this theoretical framework, the present study contextualizes the life of Rohingya women prior to displacement and as refugees in India. It aims to assess the de jure and de facto rights of these women through the process of displacement. Moving beyond rigid assertions, this study postulates that refugeehood does not mean a complete absence of decision-making spaces for Rohingya women nor does it in any way mean a sudden disappearance of their sufferings. It focuses on their experiences as women and steers clear of homogenizing their narratives as refugees.
Pancreas-sparing tumor resection for peripancreatic paraganglioma: a case series of six patients
Authors: Sunakawa Taiki , Kobayashi Shin , Kudo Masashi , Sugimoto Motokazu , Kobayashi Tatsushi , Gotohda Naoto 
Published: July 2024

Abstract
Paragangliomas (PGLs) located around the pancreas are rare and challenging to diagnose preoperatively. Tumor resection with pancreatectomy is often performed for peripancreatic PGL. However, pancreas-sparing tumor resection can be indicated with an accurate preoperative diagnosis. Six patients with pathologically diagnosed peripancreatic PGL were included. The clinical data were retrospectively collected from medical records. Five of them were suspected of peripancreatic PGL on imaging studies due to the fat plane identified between the tumor and pancreas, and subsequently diagnosed with PGL preoperatively based on elevated urinary catecholamine levels and/or metaiodobenzylguanidine scintigraphy without biopsy. All patients underwent pancreas-sparing tumor resection with negative surgical margins, and they did not develop postoperative complications related to potential damage to the pancreas. A fat plane between the tumor and pancreas on imaging studies and hormone levels are key findings for obtaining an accurate preoperative diagnosis of peripancreatic PGL, which can be managed with pancreas-sparing tumor resection.
GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs
Authors: Zhao Jianshu , Both Jean Pierre , Rodriguez-R Luis M , Konstantinidis Konstantinos T 
Published: July 2024

Abstract
Genome search and/or classification typically involves finding the best-match database (reference) genomes and has become increasingly challenging due to the growing number of available database genomes and the fact that traditional methods do not scale well with large databases. By combining k-mer hashing-based probabilistic data structures (i.e. ProbMinHash, SuperMinHash, Densified MinHash and SetSketch) to estimate genomic distance, with a graph based nearest neighbor search algorithm (Hierarchical Navigable Small World Graphs, or HNSW), we created a new data structure and developed an associated computer program, GSearch, that is orders of magnitude faster than alternative tools while maintaining high accuracy and low memory usage. For example, GSearch can search 8000 query genomes against all available microbial or viral genomes for their best matches (n = ∼318 000 or ∼3 000 000, respectively) within a few minutes on a personal laptop, using ∼6 GB of memory (2.5 GB via SetSketch). Notably, GSearch has an O(log(N)) time complexity and will scale well with billions of genomes based on a database splitting strategy. Further, GSearch implements a three-step search strategy depending on the degree of novelty of the query genomes to maximize specificity and sensitivity. Therefore, GSearch solves a major bottleneck of microbiome studies that require genome search and/or classification.
Rapid functional activation of horizontally transferred eukaryotic intron-containing genes in the bacterial recipient
Authors: Yuan Wen , Yu Jing , Li Zhichao 
Published: July 2024

Abstract
Horizontal gene transfer has occurred across all domains of life and contributed substantially to the evolution of both prokaryotes and eukaryotes. Previous studies suggest that many horizontally transferred eukaryotic genes conferred selective advantages to bacterial recipients, but how these eukaryotic genes evolved into functional bacterial genes remained unclear, particularly how bacteria overcome the expressional barrier posed by eukaryotic introns. Here, we first confirmed that the presence of intron would inactivate the horizontally transferred gene in Escherichia coli even if this gene could be efficiently transcribed. Subsequent large-scale genetic screens for activation of gene function revealed that activation events could rapidly occur within several days of selective cultivation. Molecular analysis of activation events uncovered two distinct mechanisms how bacteria overcome the intron barrier: (i) intron was partially deleted and the resulting stop codon-removed mutation led to one intact foreign protein or (ii) intron was intactly retained but it mediated the translation initiation and the interaction of two split small proteins (derived from coding sequences up- and downstream of intron, respectively) to restore gene function. Our findings underscore the likelihood that horizontally transferred eukaryotic intron-containing genes could rapidly acquire functionality if they confer a selective advantage to the prokaryotic recipient.
A novel real-time model for predicting acute kidney injury in critically ill patients within 12 hours
Authors: Sun Tao , Yue Xiaofang , Chen Xiao , Huang Tiancha , Gu Shaojun , Chen Yibing , Yu Yang , Qian Fang , Han Chunmao , Pan Xuanliang , Lu Xiao , Li Libin , Ji Yun , Wu Kangsong , Li Hongfu , Zhang Gong , Li Xiang , Luo Jia , Huang Man , Cui Wei , Zhang Mao , Tao Zhihua 
Published: July 2024

ABSTRACT

Background
A major challenge in the prevention and early treatment of acute kidney injury (AKI) is the lack of high-performance predictors in critically ill patients. Therefore, we innovatively constructed U-AKIpredTM for predicting AKI in critically ill patients within 12 h of panel measurement.

Methods
The prospective cohort study included 680 patients in the training set and 249 patients in the validation set. After performing inclusion and exclusion criteria, 417 patients were enrolled in the training set and 164 patients were enrolled in the validation set. AKI was diagnosed by Kidney Disease: Improving Global Outcomes (KDIGO) criteria.

Results
Twelve urinary kidney injury biomarkers (mALB, IgG, TRF, α1MG, NAG, NGAL, KIM-1, L-FABP, TIMP2, IGFBP7, CAF22, and IL-18) exhibited good predictive performance for AKI within 12 h in critically ill patients. U-AKIpredTM, combined with three crucial biomarkers (α1MG, L-FABP, and IGFBP7) by multivariate logistic regression analysis, exhibited better predictive performance for AKI in critically ill patients within 12 h than the other 12 kidney injury biomarkers. The area under the curve (AUC) of the U-AKIpredTM, as a predictor of AKI within 12 h, was 0.802 (95% CI: 0.771–0.833, P &lt; .001) in the training set and 0.844 (95% CI: 0.792–0.896, P &lt; .001) in the validation cohort. A nomogram based on the results of the training and validation sets of U-AKIpredTM was developed that showed optimal predictive performance for AKI. The fitting effect and prediction accuracy of U-AKIpredTM was evaluated by multiple statistical indicators. To provide a more flexible predictive tool, the dynamic nomogram (https://www.xsmartanalysis.com/model/U-AKIpredTM) was constructed using a web calculator. Decision curve analysis and a clinical impact curve were used to reveal that U-AKIpredTM with the three crucial biomarkers had a higher net benefit than these 12 kidney injury biomarkers, respectively. The net reclassification index and integrated discrimination index were used to improve the significant risk reclassification of AKI compared with the 12 kidney injury biomarkers. The predictive efficiency of U-AKIpredTM was better than the NephroCheck® when testing for AKI and severe AKI.

Conclusion
U-AKIpredTM is an excellent predictive model of AKI in critically ill patients within 12 h and would assist clinicians in identifying those at high risk of AKI.