bluuebunny/crossref_metadata_2025_split huggingface dataset:
Domestication signatures in the non-conventional yeast
Lachancea cidri
Authors: Villarreal Pablo , O'Donnell Samuel , Agier Nicolas , Muñoz-Guzman Felipe , Benavides-Parra Jose , Urbina Kami , Peña Tomas A. , Solomon Mark , Nespolo Roberto F. , Fischer Gilles , Varela Cristian , Cubillos Francisco A. 
Published: December 2023

ABSTRACT

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a
Lachancea cidri
yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain’s phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the
L. cidri
CBS2950. In addition, the large reciprocal translocation affects a proline permease (
PUT4
) regulatory region, resulting in higher
PUT4
transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.

IMPORTANCE

The exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as
Saccharomyces cerevisiae
, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in
Lachancea cidri
, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.
Evidence for novel polycyclic aromatic hydrocarbon degradation pathways in culturable marine isolates
Authors: Walton Jillian L. , Buchan Alison 
Published: December 2023

ABSTRACT

Polycyclic aromatic hydrocarbons (PAHs) are common toxic and carcinogenic pollutants in marine ecosystems. Despite their prevalence in these habitats, relatively little is known about the natural microflora and biochemical pathways that contribute to their degradation. Approaches to investigate marine microbial PAH degraders often heavily rely on genetic biomarkers, which requires prior knowledge of specific degradative enzymes and genes encoding them. As such, these biomarker-reliant approaches cannot efficiently identify novel degradation pathways or degraders. Here, we screen 18 marine bacterial strains representing the Pseudomonadota, Bacillota, and Bacteroidota phyla for degradation of two model PAHs, pyrene (high molecular weight) and phenanthrene (low molecular weight). Using a qualitative PAH plate screening assay, we determined that 16 of 18 strains show some ability to degrade either or both compounds. Degradative ability was subsequently confirmed with a quantitative high-performance liquid chromatography approach, where an additional strain showed some degradation in liquid culture. Several members of the prominent marine
Roseobacteraceae
family degraded pyrene and phenanthrene with varying efficiency (1.2%–29.6% and 5.2%–52.2%, respectively) over 26 days. Described PAH genetic biomarkers were absent in all PAH degrading strains for which genome sequences are available, suggesting that these strains harbor novel transformation pathways. These results demonstrate the utility of culture-based approaches in expanding the knowledge landscape concerning PAH degradation in marine systems.

IMPORTANCE
Polycyclic aromatic hydrocarbon (PAH) pollution is widespread throughout marine environments and significantly affects native flora and fauna. Investigating microbes responsible for degrading PAHs in these environments provides a greater understanding of natural attenuation in these systems. In addition, the use of culture-based approaches to inform bioinformatic and omics-based approaches is useful in identifying novel mechanisms of PAH degradation that elude genetic biomarker-based investigations. Furthermore, culture-based approaches allow for the study of PAH co-metabolism, which increasingly appears to be a prominent mechanism for PAH degradation in marine microbes.
PlAtg8-mediated autophagy regulates vegetative growth, sporangial cleavage, and pathogenesis in
Peronophythora litchii
Authors: Yu Ge , Li Wenqiang , Yang Chengdong , Zhang Xue , Luo Manfei , Chen Taixu , Wang Xuejian , Wang Rongbo , Chen Qinghe 
Published: December 2023

ABSTRACT

Autophagy is a conserved cellular metabolic process in eukaryotes that transports damaged or redundant intracellular organelles and proteins to lysosomes or vacuoles for degradation and recycling. Atg8 is not only essential for autophagosome formation but also required for fungal development and pathogenicity, but its function is unknown in
Peronophythora litchii
. In this study, PlAtg8, a yeast Atg8 homolog, is deleted by the CRISPR/Cas9 system coupled with PEG-mediated protoplast transformation in
P. litchii
. Compared with the wild-type strain, the absence of PlAtg8 affects autophagosome formation. The colony growth rate, number of sporangia, and zoospore release rate are significantly decreased, and the oospores are undetected in Δ
Platg8
. The pathogenicity test shows that the lesion areas on litchi leaves and fruits caused by Δ
Platg8
are significantly attenuated compared with the wild type, indicating that PlAtg8 is also required for the pathogenicity of
P. litchii
. Moreover, the cleavage rate of sporangia in Δ
Platg8
is significantly decreased compared to the wild type by FM4-64 staining, which is probably the main reason for the lower zoospores release rate in Δ
Platg8
. These results suggest that PlAtg8 not only regulates autophagy but also participates in the growth and development of
P. litchii
.

IMPORTANCE

Peronophythora litchii
is the pathogen of litchi downy blight, which is the most serious disease in litchi. Autophagy is an evolutionarily conserved catabolic process in eukaryotes. Atg8 is a core protein of the autophagic pathway, which modulates growth and pathogenicity in the oomycete
P. litchii
. In
P. litchii
, CRISPR/Cas9-mediated knockout of the
PlATG8
impaired autophagosome formation.
PlATG8
knockout mutants exhibited attenuated colony expansion, sporangia production, zoospore discharge, and virulence on litchi leaves and fruits. The reduction in zoospore release was likely underpinned by impaired sporangial cleavage. Thus, in addition to governing autophagic flux, PlAtg8 is indispensable for vegetative growth and infection of
P. litchii
.
Supplemental Material: Early uplift and exhumation of the Tanggula granitoid pluton since the Late Cretaceous: Implications for the stepwise topographic growth model in the eastern Qiangtang terrane
Authors: Lu Lu , et al.  
Published: December 2023

<p>Table S1: A compilation of low-temperature thermochronology (LTT) data in the eastern Qiangtang terrane. Table S2: Apatite U-Pb dating results for samples from the Tanggula granitoid pluton. Table S3: Biotite <sup>40</sup>Ar-<sup>39</sup>Ar furnace step-heating analytical results for samples from the Tanggula granitoid pluton. Table S4: K-feldspar <sup>40</sup>Ar-<sup>39</sup>Ar furnace step-heating analytical results for samples from the Tanggula granitoid pluton. Table S5: Zircon fission-track data of samples from the Tanggula granitoid pluton. Table S6: Apatite fission-track data of samples from the Tanggula granitoid pluton. Table S7: Single-grain zircon (U-Th)He data of samples from the Tanggula granitoid pluton. </p>
Safety and efficacy of a nitrous oxide procedural sedation programme in a paediatric emergency department: a decade of outcomes
Authors: Croughan Sean , Barrett Michael , O'Sullivan Ronan , Beegan Aidan , Blackburn Carol 
Published: December 2023

BackgroundNitrous oxide (N2O) has multiple benefits in paediatric procedural sedation (PPS), but use is restricted by its limited analgesic properties. Analgesic potency could be increased by combining N2O and intranasal fentanyl (INF). We assessed safety and efficacy data from 10 years (2011–2021) of our N2O PPS programme.MethodsProspectively collected data from a sedation registry at a paediatric emergency department (PED) were reviewed. Total procedures performed with N2O alone or with INF, success rate, sedation depth and adverse events were determined. Contributing factors for these outcomes were assessed via regression analysis and compared between different N2O concentrations, N2O in combination with INF, and for physician versus nurse administered sedation. A post hoc analysis on factors associated with vomiting was also performed.Results831 N2O procedural sedations were performed, 358 (43.1%) involved a combination INF and N2O. Nurses managed sedation in 728 (87.6%) cases. Median sedation depth on the University of Michigan Sedation Scale was 1 (IQR 1–2). Sedation was successful in 809 (97.4%) cases. Combination INF/N2O demonstrated higher median sedation scores (2 vs 1, p<0.001) and increased vomiting (RR 1.8, 95% CI 1.3 to 2.5), with no difference in sedation success compared with N2O alone. No serious adverse events (SAEs) were reported (desaturation, apnoea, aspiration, bradycardia or hypotension) regardless of N2O concentration or use of INF. 137 (16.5%) minor adverse events occurred. Vomiting occurred in 113 (13.6%) cases and was associated with higher concentrations of N2O and INF use, but not associated with fasting status. There were no differences in adverse events (RR 0.98, 95% CI 0.97 to 1.04) or success rates (RR 0.93, 95% CI 0.56 to 1.7) between physician provided and nurse provided sedation.ConclusionN2O can provide effective PED PPS. No SAEs were recorded. INF may be an effective PPS adjunct but remains limited by increased rates of vomiting.
Evolving educational landscape in pathology: a comprehensive bibliometric and visual analysis including digital teaching and learning resources
Authors: Cima Luca , Bussola Nicole , Hassell Lewis A , Kiehl Tim-Rasmus , Schukow Casey , Zerbe Norman , Munari Enrico , Torresani Evelin , Barbareschi Mattia , Cecchini Matthew J , Cirielli Vito , Pagliuca Francesca , Ahsan Muhammad , Mohanty Sambit K , Arbitrio Ernesto , Hughes Griffin , Mirza Kamran M 
Published: December 2023

AimsPathology education is a core component of medical training, and its literature is critical for refining educational modalities. We performed a cross-sectional bibliometric analysis to explore publications on pathology education, focusing on new medical education technologies.MethodsThe analysis identified 64 pathology journals and 53 keywords. Relevant articles were collected using a web application, PaperScraper, developed to accelerate literature search. Citation data were collected from multiple sources. Descriptive statistics, with time period analysis, were performed using Microsoft Excel and visualised with Flourish Studio. Two article groups were further investigated with a bibliometric software, VOSViewer, to establish co-authorship and keyword relationships.Results8946 citations were retrieved from 905 selected articles. Most articles were published in the last decade (447, 49.4%). The top journals wereArchives of Pathology & Laboratory Medicine(184),Human Pathology(122) and theAmerican Journal of Clinical Pathology(117). The highest number of citations was found forHuman Pathology(2120), followed byArchives of Pathology & Laboratory Medicine(2098) andAmerican Journal of Clinical Pathology(1142). Authors with different backgrounds had the greatest number of articles and citations. 12 co-authorship, 3 keyword and 8 co-citation clusters were found for the social media/online resources group, 8 co-authorship, 4 keyword and 7 co-citation clusters for the digital pathology/virtual microscopy/mobile technologies group.ConclusionsThe analysis revealed a significant increase in publications over time. The emergence of digital teaching and learning resources played a major role in this growth. Overall, these findings underscore the transformative potential of technology in pathology education.
Exact rotating black hole solutions for f(R) gravity by modified Newman Janis algorithm
Authors: Chaturvedi Pankaj , Kumar Utkarsh , Thattarampilly Udaykrishna , Kakkat Vishnu 
Published: December 2023

AbstractWe show that the f(R)-gravity theories with constant Ricci scalar in the Jordan/Einstein frame can be described by Einstein or Einstein–Maxwell gravity with a cosmological term and a modified gravitational constant. To obtain the rotating axisymmetric solutions for the Einstein/Einstein–Maxwell gravity with a cosmological constant, we also propose a modified Newmann–Janis algorithm which involves the non-complexification of the radial coordinate and a complexification of the polar coordinate. Using the duality between the two gravity theories we show that the stationary or static solutions for the Einstein/Einstein–Maxwell gravity with a cosmological constant will also be the solutions for the dual f(R)-gravity with constant Ricci scalar.
UPQC-Based Hybrid Technique to Reduce Power Quality Problems in the Photovoltaic Grid System
Authors: Shankar C. Udhaya , Nithya devi N. 
Published: December 2023

In addition to Power Quality (PQ) problems caused by solid state devices in the distribution side of grid connected Photo Voltaic (PV) system, quality of power also suffers in the source side by the usage of converters. Generally, PQ problems mitigation strategy has turned into a critical issue in grid-connected PV systems. This paper proposes a control topology for PQ issues mitigation scheme in grid connected PV systems. The primary goal of this study is to enhance the PQ in power distribution system through eradicating the voltage interruption, voltage swell and sag as well as voltage fluctuation. To accomplish these changes, Unified Power Quality Conditioners (UPQCs) with controllers were utilized. Then the faults are mitigated by the utilization of UPQC with Tree Seeds Algorithm (TSA) — Adaptive Neuro-Fuzzy Interference System (ANFIS). At first, the normal properties of the grid-connected PV systems are dissected. From that point forward, a few interruptions are made in the system and the abnormal characteristics are analyzed. Then the abnormal characteristics of PQ problems are diminished in the utilization of UPQC and TSA–ANFIS controllers. UPQC is one of the best filters topologies which can mitigate and control all PQ problems. The combined algorithms of TSA-ANFIS are used to keep the dc-link voltage in UPQC at consistent level. The proposed hybrid approach is executed in MATLAB/Simulink platform and the performance is studied. Further, the proposed method is compared with existing Elephant Herding Optimization (EHO) technique and also with hybrid EHO-ANFIS techniques. The comparison results showed that the proposed technique is superior to the EHO and EHO-ANFIS techniques.
Rethinking the Encoding of Integers for Scans on Skewed Data
Authors: Prammer Martin , Patel Jignesh M. 
Published: December 2023

Bit-parallel scanning techniques are characterized by their ability to accelerate compute through the process known as early pruning. Early pruning techniques iterate over the bits of each value, searching for opportunities to safely prune compute early, before processing each data value in its entirety. However, because of this iterative evaluation, the effectiveness of early pruning depends on the relative position of bits that can be used for pruning within each value. Due to this behavior, bit-parallel techniques have faced significant challenges when processing skewed data, especially when values contain many leading zeroes. This problem is further amplified by the inherent trade-off that bit-parallel techniques make between columnar scan and fetch performance: a storage layer that supports early pruning requires multiple memory accesses to fetch a single value. Thus, in the case of skewed data, bit-parallel techniques increase fetch latency without significantly improving scan performance when compared to baseline columnar implementations.
To remedy this shortcoming, we transform the values in bit-parallel columns using novel encodings. We propose the concept of forward encodings: a family of encodings that shift pruning-relevant bits closer to the most significant bit. Using this concept, we propose two particular encodings: the Data Forward Encoding and the Extended Data Forward Encoding. We demonstrate the impact of these encodings using multiple real-world datasets. Across these datasets, forward encodings improve the current state-of-the-art bit-parallel technique's scan and fetch performance in many cases by 1.4x and 1.3x, respectively.
Solo: Data Discovery Using Natural Language Questions Via A Self-Supervised Approach
Authors: Wang Qiming , Castro Fernandez Raul 
Published: December 2023

Most deployed data discovery systems, such as Google Datasets, and open data portals only support keyword search. Keyword search is geared towards general audiences but limits the types of queries the systems can answer. We propose a new system that lets users write natural language questions directly. A major barrier to using this learned data discovery system is it needs expensive-to-collect training data, thus limiting its utility.
In this paper, we introduce a self-supervised approach to assemble training datasets and train learned discovery systems without human intervention. It requires addressing several challenges, including the design of self-supervised strategies for data discovery, table representation strategies to feed to the models, and relevance models that work well with the synthetically generated questions. We combine all the above contributions into a system, Solo, that solves the problem end to end. The evaluation results demonstrate the new techniques outperform state-of-the-art approaches on well-known benchmarks. All in all, the technique is a stepping stone towards building learned discovery systems.
Lightweight Acquisition and Ranging of Flows in the Data Plane
Authors: Monterubbiano Andrea , Langlet Jonatan , Walzer Stefan , Antichi Gianni , Reviriego Pedro , Pontarelli Salvatore 
Published: December 2023

As networks get more complex, the ability to track almost all the flows is becoming of paramount importance. This is because we can then detect transient events impacting only a subset of the traffic. Solutions for flow monitoring exist, but it is getting very difficult to produce accurate estimations for every <flowID,counter> tuple given the memory constraints of commodity programmable switches. Indeed, as networks grow in size, more flows have to be tracked, increasing the number of tuples to be recorded. At the same time, end-host virtualization requires more specific flowIDs, enlarging the memory cost for every single entry. Finally, the available memory resources have to be shared with other important functions as well (e.g., load balancing, forwarding, ACL).
To address those issues, we present FlowLiDAR (Flow Lightweight Detection and Ranging), a new solution that is capable of tracking almost all the flows in the network while requiring only a modest amount of data plane memory which is not dependent on the size of flowIDs. We implemented the scheme in P4, tested it using real traffic from ISPs and compared it against four state-of-the-art solutions: FlowRadar, NZE, PR-sketch, and Elastic Sketch. While those can only reconstruct up to 60% of the tuples, FlowLiDAR can track 98.7% of them with the same amount of memory.
Nautilus: A Framework for Cross-Layer Cartography of Submarine Cables and IP Links
Authors: Ramanathan Alagappan , Abdu Jyothi Sangeetha 
Published: December 2023

Submarine cables constitute the backbone of the Internet. However, these critical infrastructure components are vulnerable to several natural and man-made threats, and during failures, are difficult to repair in remote oceans. In spite of their crucial role, we have a limited understanding of the impact of submarine cable failures on global connectivity, particularly on the higher layers of the Internet.
In this paper, we present Nautilus, a framework for cross-layer cartography of submarine cables and IP links. Using a corpus of public datasets and Internet cartographic techniques, Nautilus identifies IP links that are likely traversing submarine cables and maps them to one or more potential cables. Nautilus also gives each IP to cable assignment a prediction score that reflects the confidence in the mapping. Nautilus generates a mapping for 3.05 million and 1.43 million IPv4 and IPv6 links, respectively, spanning 91% of all active cables. In the absence of ground truth data, we validate Nautilus mapping using three techniques: analyzing past cable failures, using targeted traceroute measurements, and comparing with public network maps of two operators.
Near-Optimal Stochastic Bin-Packing in Large Service Systems with Time-Varying Item Sizes
Authors: Hong Yige , Xie Qiaomin , Wang Weina 
Published: December 2023

In modern computing systems, jobs' resource requirements often vary over time. Accounting for this temporal variability during job scheduling is essential for meeting performance goals. However, theoretical understanding on how to schedule jobs with time-varying resource requirements is limited. Motivated by this gap, we propose a new setting of the stochastic bin-packing problem in service systems that allows for time-varying job resource requirements, also referred to as 'item sizes' in traditional bin-packing terms. In this setting, a job or 'item' must be dispatched to a server or 'bin' upon arrival. Its resource requirement may vary over time while in service, following a Markovian assumption. Once the job's service is complete, it departs from the system. Our goal is to minimize the expected number of active servers, or 'non-empty bins', in steady state.
Under our problem formulation, we develop a job dispatch policy, named Join-Reqesting-Server (JRS). Broadly, JRS lets each server independently evaluate its current job configuration and decide whether to accept additional jobs, balancing the competing objectives of maximizing throughput and minimizing the risk of resource capacity overruns. The JRS dispatcher then utilizes these individual evaluations to decide which server to dispatch each arriving job to. The theoretical performance guarantee of JRS is in the asymptotic regime where the job arrival rate scales large linearly with respect to a scaling factor r. We show that JRS achieves an additive optimality gap of O(√r) in the objective value, where the optimal objective value is Θ(r). When specialized to constant job resource requirements, our result improves upon the state-of-the-art o(r) optimality gap. Our technical approach highlights a novel policy conversion framework that reduces the policy design problem into a single-server problem.