bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geometric and isometric properties of two classes of sequence spaces
Authors: Botelho Fernanda , Kazemi Sana 
Published: November 2022

We study geometric and isometric properties of two classes of sequence spaces. First, we consider the Banach sequence space

X
n

X_n

, the completion of

c

00

c_{00}

relatively to the norm
\[

‖
x

‖
n

=
sup

{

∑

i
∈
F

|

x
i

|

,
with
,
F
of cardinality at most
n
}

.

\|x\|_n = \sup \left \{\sum _{i \in F}|x_i|, \text { with }, F \text { of cardinality at most } n\right \}.

\]
For this space, we show that the isometry group of

X
n

X_n

consists of standard isometries. Second, we consider a Tsirelson-type space,

T
[
θ
,

A
n

]

T[\theta , A_n]

(

0
>
θ
>
1

0>\theta >1

) associated with the regular family

A
n

A_n

, comprised of all subsets of

N

\mathbb {N}

with at most

n
n

elements. For this space, we characterize the extreme points and show that for

θ
≤

1
n

\theta \leq \frac {1}{n}

,

T
[
θ
,

A
n

]

T[\theta , A_n]

supports standard isometries. We also derive the form for the surjective isometries of

T
[
θ
,

A
3

]

T[\theta , A_3]

.
GPU-accelerated and pipelined methylation calling
Authors: Feng Yilin , Gudukbay Akbulut Gulsum , Tang Xulong , Gunasekaran Jashwant Raj , Rahman Amatur , Medvedev Paul , Kandemir Mahmut 
Published: November 2022

Abstract

Motivation
The third-generation DNA sequencing technologies, such as Nanopore Sequencing, can operate at very high speeds and produce longer reads, which in turn results in a challenge for the computational analysis of such massive data. Nanopolish is a software package for signal-level analysis of Oxford Nanopore sequencing data. Call-methylation module of Nanopolish can detect methylation based on Hidden Markov Model (HMM). However, Nanopolish is limited by the long running time of some serial and computationally expensive processes. Among these, Adaptive Banded Event Alignment (ABEA) is the most time-consuming step, and the prior work, f5c, has already parallelized and optimized ABEA on GPU. As a result, the remaining methylation score calculation part, which uses HMM to identify if a given base is methylated or not, has become the new performance bottleneck.

Results
This article focuses on the call-methylation module that resides in the Nanopolish package. We propose Galaxy-methyl, which parallelizes and optimizes the methylation score calculation step on GPU and then pipelines the four steps of the call-methylation module. Galaxy-methyl increases the execution concurrency across CPUs and GPUs as well as hardware resource utilization for both. The experimental results collected indicate that Galaxy-methyl can achieve 3×–5× speedup compared with Nanopolish, and reduce the total execution time by 35% compared with f5c, on average.

Availability and implementation
The source code of Galaxy-methyl is available at https://github.com/fengyilin118/.
SCExecute: custom cell barcode-stratified analyses of scRNA-seq data
Authors: Edwards Nathan , Dillard Christian , Prashant N M , Hongyu Liu , Yang Mia , Ulianova Evgenia , Horvath Anelia 
Published: November 2022

Abstract

Motivation
In single-cell RNA-sequencing (scRNA-seq) data, stratification of sequencing reads by cellular barcode is necessary to study cell-specific features. However, apart from gene expression, the analyses of cell-specific features are not sufficiently supported by available tools designed for high-throughput sequencing data.

Results
We introduce SCExecute, which executes a user-provided command on barcode-stratified, extracted on-the-fly, single-cell binary alignment map (scBAM) files. SCExecute extracts the alignments with each cell barcode from aligned, pooled single-cell sequencing data. Simple commands, monolithic programs, multi-command shell scripts or complex shell-based pipelines are then executed on each scBAM file. scBAM files can be restricted to specific barcodes and/or genomic regions of interest. We demonstrate SCExecute with two popular variant callers—GATK and Strelka2—executed in shell-scripts together with commands for BAM file manipulation and variant filtering, to detect single-cell-specific expressed single nucleotide variants from droplet scRNA-seq data (10X Genomics Chromium System).
In conclusion, SCExecute facilitates custom cell-level analyses on barcoded scRNA-seq data using currently available tools and provides an effective solution for studying low (cellular) frequency transcriptome features.

Availability and implementation
SCExecute is implemented in Python3 using the Pysam package and distributed for Linux, MacOS and Python environments from https://horvathlab.github.io/NGS/SCExecute.

Supplementary information
Supplementary data are available at Bioinformatics online.
Biotechnology Immersion Program: professional development where the participants do the preparation, teaching, and outreach to maximize learning gains
Authors: Bates Katherine L , Hung Chia , Steel J Jordan 
Published: November 2022

Abstract
Professional development for teachers of primary, intermediate, and secondary schools (Kindergarten to Grade 12; K-12), especially for highly technical subjects such as Microbial Biotechnology, can involve arduous and ineffective training methods prioritizing content delivery over sound pedagogical techniques. Teachers are learning complex content, techniques, and pedagogies but have little time to practice or gain experience and confidence in their newly acquired skills. The Biotechnology Immersion Program (BiP) sought to overcome this challenge by incorporating an intentional immersive experiential system into professional development; teachers learn new content, experience hands-on activities, and work through assessments in the role of a student while experienced subject matter expert faculty run the teaching and activities. Afterwards, the teachers get the opportunity to switch roles and practice teaching, running, and managing the same learning activities that they just experienced. The faculty experts are available to mentor, guide, and direct the teachers as they try out teaching and implementing novel biotechnology classroom activities. BiP focused on three critical aspects of successful professional development: time, personal experience, and connection. This mentored teaching and implementation practice system provided a robust professional development platform, where educators felt prepared and confident to run new biotechnology lab activities in their own classrooms.
Strategies for change: thriving as an individual with a disabilty in STEMM
Authors: Crabtree Amber , Neikirk Kit , Marshall Andrea , Barongan Taylor , Beasley Heather K , Lopez Edgar Garza , Stephens Dominique , Murray Sandra , Spencer Elsie C , Martinez Denise , Vang Chia , Jenkins Felysha , Damo Steven , Vue Zer 
Published: November 2022

AbstractDisability remains an underacknowledged and underdiscussed topic in science, technology, engineering, mathematics, and medicine (STEMM). Social stigma and fear of negative outcomes have resulted in a consistent lack of disclosure. Disabilities cause social and professional difficulties for those that have them. While some faculty can be allies, past literature shows that steps must be taken to make disabilities visible in STEMM at both student and faculty levels. Here, we offer suggestions to better support faculty and students in enhancing the outcomes of individuals who have invisible disabilities. Critically, techniques such as abolishing stigma, universal learning, and better mentoring may improve the challenges faced by those who self-identify as an individual with a disability.
Early-life starvation alters lipid metabolism in adults to cause developmental pathology in Caenorhabditis elegans
Authors: Jordan James M , Webster Amy K , Chen Jingxian , Chitrakar Rojin , Ryan Baugh L 
Published: November 2022

Abstract
Early-life malnutrition increases adult disease risk in humans, but the causal changes in gene regulation, signaling, and metabolism are unclear. In the roundworm Caenorhabditis elegans, early-life starvation causes well-fed larvae to develop germline tumors and other gonad abnormalities as adults. Furthermore, reduced insulin/IGF signaling during larval development suppresses these starvation-induced abnormalities. How early-life starvation and insulin/IGF signaling affect adult pathology is unknown. We show that early-life starvation has pervasive effects on adult gene expression which are largely reversed by reduced insulin/IGF signaling following recovery from starvation. Early-life starvation increases adult fatty-acid synthetase fasn-1 expression in daf-2 insulin/IGF signaling receptor-dependent fashion, and fasn-1/FASN promotes starvation-induced abnormalities. Lipidomic analysis reveals increased levels of phosphatidylcholine in adults subjected to early-life starvation, and supplementation with unsaturated phosphatidylcholine during development suppresses starvation-induced abnormalities. Genetic analysis of fatty-acid desaturases reveals positive and negative effects of desaturation on development of starvation-induced abnormalities. In particular, the ω3 fatty-acid desaturase fat-1 and the Δ5 fatty-acid desaturase fat-4 inhibit and promote development of abnormalities, respectively. fat-4 is epistatic to fat-1, suggesting that arachidonic acid–containing lipids promote development of starvation-induced abnormalities, and supplementation with ARA enhanced development of abnormalities. This work shows that early-life starvation and insulin/IGF signaling converge on regulation of adult lipid metabolism, affecting stem-cell proliferation and tumor formation.
Enigmatic doubly scattered tube waves at a crosswell seismic survey
Authors: Nakata Nori , Nakata Rie , Kato Ayato , Xue Ziqiu , White Malcolm C A 
Published: November 2022

SUMMARY
Enigmatically strong tube waves continue to exist long after the direct wave during repeat crosswell-monitoring surveys at the Nagaoka CO2 injection site in Japan. The tube waves, which have linear moveouts with velocities of 1.29 and 1.41 km s−1 at plastic and steel casings, respectively, are generated by double scattering on the shallow side of the wells. We characterize wavefields to confirm that these late coda waves are tube waves that are excited at the source well, propagate upward, then travel to a receiver well as a body wave, and finally propagate downward along the receiver well. Even though these tube waves result from second-order scattering, they have large amplitudes because of the relatively short distance between source and receiver wells. Because these waves propagate along both wells many times, we can extract detailed information of wave propagation by averaging them to increase the signal-to-noise ratio. We first use the tube waves to relocate sources and receivers between multiple monitoring surveys, demonstrating our ability to correct the severe noise caused by location errors that frequently degrades the repeatability of time-lapse surveys. Then, we apply an inversion based on the physics of tube waves to estimate the location and strength of the scatterers and find that they are predominantly located in the shallow segment of the wells, above the sources, and infer that they are related to local fractures and/or wellbore conditions because their locations do not correspond to the well geometry. Lastly, we use the tube waves to accurately estimate subsurface velocities along the wells. The estimation is stable and robust, and the velocities follow the general trend of subsurface structure seen in the well log data. Due to the receiver spacing, tube-wave analysis cannot resolve a thin, high-velocity layer at the CO2 reservoir. By combining tube waves observed during different stages of the monitoring survey, we can estimate the time-lapse changes of the subsurface velocities.
Subject Matter Jurisdiction
Authors: Klein Natalie , Parlett Kate 
Published: November 2022

Abstract
This chapter examines the judicial decisions relating to subject matter jurisdiction in cases arising under the UN Convention on the Law of the Sea (UNCLOS). It analyses the characterisation of disputes to determine if they concern the interpretation or application of UNCLOS, particularly asking whether territorial sovereignty disputes may be resolved in UNCLOS dispute settlement. Questions of incidental jurisdiction are considered. The chapter addresses possible jurisdictional limitations in relation to disputes concerning fishing and the marine environment. The discussion also assesses the optional exceptions to compulsory jurisdiction under UNCLOS, which include maritime boundary delimitation disputes, historic bays, and historic title disputes, as well as disputes concerning military activities and certain law enforcement activities. The final part of the chapter examines the difference between applicable law and subject matter jurisdiction, and the relevance of renvoi and rules of reference in UNCLOS for jurisdiction.
Maritime Space
Authors: Klein Natalie , Parlett Kate 
Published: November 2022

Abstract
This chapter analyses judicial decisions arising under the UN Convention on the Law of the Sea that have been concerned with rights and duties in different maritime zones and the baselines from which those zones are measured. The chapter examines the definitions of low-tide elevations, rocks, and islands in light of the different maritime entitlements of these features. Cases that have assessed the drawing of baselines and designation of basepoints for asserting maritime zones are considered. This chapter further considers judicial decisions on the nature of the different maritime zones, such as internal waters, territorial sea, exclusive economic zone, and continental shelf, as a way to explore the core rights and duties of States within these zones. This discussion is developed in later chapters in Judging the Law of the Sea.
Fisheries
Authors: Klein Natalie , Parlett Kate 
Published: November 2022

Abstract
This chapter analyses judicial decisions that have bearing on international fisheries and their regulation under the UN Convention on the Law of the Sea (UNCLOS). The chapter first assesses decisions relating to traditional fishing and then turns to fishing in the territorial sea. Despite jurisdictional limitations, there have been several notable judicial proceedings examining rights and obligations relating to fishing in the exclusive economic zone (EEZ). The chapter considers the scope of sovereign rights over fishing in the EEZ, the content of obligations relating to the conservation and utilisation of living resources in the EEZ, and due diligence standards. Disputes have also emerged in relation to law enforcement of fisheries regulations in the EEZ and have been addressed on the merits as well as in the context of prompt release proceedings under Article 292 of UNCLOS. The chapter discusses the small amount of case law on straddling stocks and highly migratory species before turning to fisheries disputes on the high seas and what judicial consideration has emerged in relation to the UNCLOS provisions dealing with the conservation and management of high seas fisheries.
A multidisciplinary management algorithm for brain metastases
Authors: Ramos Alexander , Giantini-Larsen Alexandra , Pannullo Susan C , Brandmaier Andrew , Knisely Jonathan , Magge Rajiv , Wilcox Jessica A , Pavlick Anna C , Ma Barbara , Pisapia David , Ashamalla Hani , Ramakrishna Rohan 
Published: November 2022

Abstract
The incidence of brain metastases continues to present a management issue despite the advent of improved systemic control and overall survival. While the management of oligometastatic disease (ie, 1–4 brain metastases) with surgery and radiation has become fairly straightforward in the era of radiosurgery, the management of patients with multiple metastatic brain lesions can be challenging. Here we review the available evidence and provide a multidisciplinary management algorithm for brain metastases that incorporates the latest advances in surgery, radiation therapy, and systemic therapy while taking into account the latest in precision medicine-guided therapies. In particular, we argue that whole-brain radiation therapy can likely be omitted in most patients as up-front therapy.
The temporal dynamics of antimicrobial-resistant Salmonella enterica and predominant serovars in China
Authors: Wang Yanan , Liu Yue , Lyu Na , Li Zhiyuan , Ma Sufang , Cao Demin , Pan Yuanlong , Hu Yongfei , Huang Hua , Gao George F , Xu Xuebin ,   the Bacterium-learning Union, Zhu Baoli 
Published: November 2022

ABSTRACT
Salmonella enterica is one of the most common bacterial pathogens in humans and animals. Systematic studies on the trends and geographical distribution of antimicrobial-resistant Salmonella and dominant serovars have been well studied in European and American countries while not in China. Here, taking the One-Health strategy, we used &gt;35 000 Salmonella enterica isolates to explore the temporal and spatial dynamics of dominant serovars in China. We found that Salmonella Typhimurium was the dominant serovar causing human infection in China, which was consistent with Australia but inconsistent with North American and European countries. The proportion of Salmonella serovars Typhimurium, London, Rissen, Corvallis, Meleagridis, Kentucky, and Goldcoast showed an increasing trend during 2006–2019. We randomly selected 1962 isolates for comparative genomics and antimicrobial resistance studies and found that the number of antibiotic resistance genes (ARGs) per isolate increased 1.84 and 2.69 times of human and non-human origins, respectively, spanning 14 years. The proportion of antimicrobial-resistant Salmonella isolates had an increasing trend during 2006–2019, especially beta-lactam, quinolone, tetracycline, and rifampicin resistance. Moreover, we found that higher diversity of sequence types (STs) in S. Typhimurium than in other serovars, ST34 from pig and ST19 from chicken origin, were mainly associated with isolates causing child and adult gastro-infection, respectively. Our results fill in the data gap on the trends of dominant serovars and antimicrobial resistance of Salmonella enterica in China. These data provide useful information for public health decision-makers prioritizing interventions for foodborne diseases and food safety.
The ultracompact regions G40.54+2.59 and G34.13+0.47: A new detection of compact radio sources
Authors: Viveros Harold E , Masque Josep M , Trinidad Miguel A , de la Fuente Eduardo 
Published: November 2022

Abstract
We report the detection of three compact (&lt;0.001 pc) radio sources (CRSs) at the Ka-band (0.9 cm) in the ultra-compact (UC) H ii regions G040.54+2.59 (two CRSs) and G034.13+0.47 (one CRS). These CRSs have weak flux densities and are located at the center of their respective UC H ii regions. We found no clear association between massive ionizing stars and CRSs but some radiative influence on the latter, as suggested by their large emission measures (&gt;107 cm−6 pc), typical of photo-evaporating neutral objects close to or associated with massive stars. Our modelling of G40.54+2.59 shows that its CRSs supply enough ionized material to shape its morphology while significantly extending its observable lifetime. On the other hand, despite the possible relation of the CRS with the large-scale outflow signatures observed in G034.13+0.47, the influence of this CRS on the evolution of the UC H ii region is unlikely. Our results show that the presence of CRSs can alleviate the so-called lifetime problem of UC H ii regions. Still, to address the dynamical evolution of these regions adequately, the scenario must include additional mechanisms like ambient confinement, or the role of the kinematics of their associated stellar objects.
The classification of kleinian groups of hausdorff dimension at most one
Authors: Hou Yong 
Published: November 2022

Abstract
In this paper, we provide the complete classification of Kleinian group of Hausdorff dimensions less than 1. In particular, we prove that every convex cocompact Kleinian group of Hausdorff dimension &lt; 1 is a classical Schottky group. This upper bound is sharp. The result implies that the converse of Burside’s conjecture [4] is true: all non-classical Schottky groups must have Hausdorff dimension $\ge1$. The upper bounds of Hausdorff dimensions of classical Schottky groups has long been established by Phillips–Sarnak [14] and Doyle [8]. The proof of the theorem relies on the result of Bowen [3] and Hou [10].
Dynamics of recovery sleep from chronic sleep restriction
Authors: Guzzetti Jacob R , Banks Siobhan 
Published: November 2022

AbstractSleep loss is common in our 24/7 society with many people routinely sleeping less than they need. Sleep debt is a term describing the difference between the amount of sleep needed, and the amount of sleep obtained. Sleep debt can accumulate over time, resulting in poor cognitive performance, increased sleepiness, poor mood, and a higher risk for accidents. Over the last 30 years, the sleep field has increasingly focused attention on recovery sleep and the ways we can recover from a sleep debt faster and more effectively. While there are still many unanswered questions and debates about the nature of recovery sleep, such as the exact components of sleep important for recovery of function, the amount of sleep needed to recover and the impacts of prior sleep history on recovery, recent research has revealed several important attributes about recovery sleep: (1) the dynamics of the recovery process is impacted by the type of sleep loss (acute versus chronic), (2) mood, sleepiness, and other aspects of cognitive performance recover at different rates, and (3) the recovery process is complex and dependent on the length of recovery sleep and the number of recovery opportunities available. This review will summarize the current state of the literature on recovery sleep, from specific studies of recovery sleep dynamics to napping, “banking” sleep and shiftwork, and will suggest the next steps for research in this field.This paper is part of the David F. Dinges Festschrift Collection. This collection is sponsored by Pulsar Informatics and the Department of Psychiatry in the Perelman School of Medicine at the University of Pennsylvania.