bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Workflow Development for Data-Driven Neighborhood-Scale Building Performance Simulation
Authors: di Stefano Andrea Giuseppe , Ruta Matteo , Masera Gabriele , Hoque Simi 
Published: September 2024

Abstract
As urbanization intensifies, cities are key contributors to energy consumption and carbon emissions, accounting for a significant portion of global energy use and CO2 emissions. This paper introduces a systematic approach to support the development of urban projects with minimized operational carbon footprints through the integration of data-driven building performance simulation (BPS) tools in early-stage design. Emphasizing the necessity for a collaborative effort among designers, policymakers, and other stakeholders, we discuss the evolution of BPS toward incorporating data-driven tools for energy need reduction and informed decision-making. Despite the proliferation of modeling methods and data-related challenges, we present a theoretical workflow, supported by interactions with design firms in the US and European Union (EU) through interviews. This structured approach, demonstrating adaptability and scalability across urban contexts, foregrounds the potential for future data-driven integration in design practices. Grounded in theoretical concepts and preliminary real-world insights, our work emphasizes the transformation of standard activities toward data-driven processes, showcasing the crucial role of practical experience in advancing sustainable, low-carbon urban development.
Identifying
Candida auris
transmission in a hospital outbreak investigation using whole-genome sequencing and SNP phylogenetic analysis
Authors: Mitchell Brooks I. , Kling Kendall , Bolon Maureen K. , Rathod Shardul N. , Malczynski Michael , Ruiz Javier , Polanco Wanda , Fritz Kevin , Maali Sarah , Stosor Valentina , Zembower Teresa R. , Qi Chao 
Published: September 2024

ABSTRACT

Candida auris
poses a global public health challenge, causing multiple outbreaks within healthcare facilities. Despite advancements in strain typing for various infectious diseases, a consensus on the genetic relatedness threshold for identifying
C. auris
transmission in local hospital outbreaks remains elusive. We investigated genetic variations within our local isolate collection using whole-genome-based single nucleotide polymorphism (SNP) phylogenetic analysis. A total of 74
C
.
auris
isolates were subjected to whole-genome sequencing (WGS) and SNP phylogenetic analysis via the QIAGEN CLC Genomics Workbench. Isolates included known related strains from the same patient, strains from different hospitals, strains from our hospital patients with no epidemiological link, and 19 patient isolates from a recent
C. auris
outbreak. All but three isolates were identified to be Clade IV. By examining the genetic diversities of
C. auris
within patients and between patients, we identified a SNP variation range of 0–13 for identifying related isolates. During an outbreak investigation, utilizing this range, maximum likelihood phylogenetic analysis revealed two distinct clusters that aligned with the epidemiological links. Determining a SNP variation range to delineate genetic relatedness among isolates is crucial for the application of WGS and SNP phylogenetic analysis in identifying
C. auris
transmission during hospital outbreak investigations. The use of WGS SNP phylogenetic analysis via the CLC Genomics Workbench has emerged as a valuable method for typing
C. auris
in clinical microbiology laboratories.
A lipidomics-based method to eliminate negative urine culture in general population
Authors: Nartey Linda K. , Mikhael Abanoub , Pětrošová Helena , Yuen Victor , Kibsey Pamela , Pekcan Mert , Ernst Robert K. , Chen Michael X. , Goodlett David R. 
Published: September 2024

ABSTRACT

Urinary tract infections (UTIs) pose a significant challenge to human health. Accurate and timely detection remains pivotal for effective intervention. Current urine culture techniques, while essential, often encounter challenges where urinalysis yields positive results, but subsequent culture testing produces a negative result. This highlights potential discrepancies between the two methods and emphasizes the need for improved correlation in urinary tract infection (UTI) detection. Employing advanced lipidomics techniques, we deployed the fast lipid analysis technique (FLAT) on a clinical cohort suspected of having UTIs. Lipid fingerprinting by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), directly from urine samples without
ex vivo
growth, correctly identified the common uropathogens within a 1 hour timeframe when compared to urine culture. FLAT analysis also identified urine samples without culturable pathogens (negative UTIs) with 99% microbial identification (ID) agreement, whereas urinalysis showed 37% ID agreement with the gold standard urine culture. In 402 urine samples suspected for UTI from outpatients, FLAT assay rapidly ruled out negative urines without the need for culture in 77% of all cases. The potential impact of this innovative lipidomic-based approach extends beyond conventional diagnostic limitations, offering new avenues for early detection and targeted management of urinary tract infections. This research marks a paradigm shift in urine culture methodology, paving the way for improved clinical outcomes and public health interventions.

IMPORTANCE
This study employs a lipidomics-based method that promises to enhance the accuracy and reliability of urine culture diagnostics within 1 hour of sample collection. Our findings underscore the potential of lipidomics as a valuable tool in identifying and characterizing microbial populations present in urine samples and efficiently rule out negative urines, ultimately leading to improved patient care and management of urinary tract infections.
Comparison of a dual antibody and antigen HCV immunoassay to standard of care algorithmic testing
Authors: Bui Tina I. , Brown Abigail P. , Brown Meghan , Lawless Sydney , Roemmich Brittany , Anderson Neil W. , Farnsworth Christopher W. 
Published: September 2024

ABSTRACT

The Centers for Disease Control and Prevention (CDC) guidelines for hepatitis C virus (HCV) testing, although effective, may miss crucial diagnostic opportunities. The goal of this study was to assess the utility of an antibody (Ab) and antigen (Ag) combination immunoassay as an alternative to traditional HCV screening. Remnant specimens from 1,341 patients with concurrent third-generation serologic (Roche anti-HCV-II) and nucleic acid amplification testing (NAAT) were assessed using the HCV Duo Ab/Ag immunoassay (Roche). Patient demographics, risk factors, and standard of care (SOC) laboratory results from the medical records were recorded. Overall, 99.0% (197/199) of the HCV Duo Ab+/Ag+specimens accurately identified active infections as confirmed by NAAT, and 99.9% (670/671) Ab−/Ag− samples corresponded to those without HCV infections. Individually, the HCV Duo Ab component demonstrated a 95.6% positive percent agreement (PPA) (95% CI = 93.8–96.9) and 99.1% negative percent agreement (NPA) (98.8–99.6) compared with SOC anti-HCV II Ab assay. The HCV Duo Ag had a 73.5% PPA (67.9–78.4) and 99.8% NPA (99.3–100) with NAAT. Among RNA+ specimens, 73.4% (197/267) were HCV Duo Ag+, and 265/267 (99.3%) were successfully detected on the HCV Duo Ab component. Notably, 5/7 (71.4%) Ab−/RNA +specimens were detected by HCV Duo, which would have been missed by traditional algorithmic testing. Fourth generation HCV Duo Ab/Ag assay demonstrated comparable performance to SOC testing and shortens the diagnostic window but does not eliminate the need for NAAT in all patients. Ab/Ag testing identified several Ab−/RNA+ cases, a subgroup often undiagnosed by current algorithmic testing, demonstrating promise for improved diagnostic efficiency and accuracy in HCV detection.

IMPORTANCE
This study highlights the potential of a combined hepatitis C virus (HCV) Duo antibody (Ab) and antigen (Ag) immunoassay to improve early detection of HCV infections. Traditional Ab−only screening methods recommended by the Centers for Disease Control and Prevention may miss early-stage infections. The HCV Duo assay showed high accuracy, detecting nearly all active infections confirmed by nucleic acid amplification testing. Dual detection of HCV Ab and Ag shortens the diagnostic window, enabling intervention and treatment in a single visit, which is crucial for improving patient outcomes and reducing HCV transmission, especially in areas with limited access to confirmatory molecular testing.
VE-1 regulation of MAPK signaling controls sexual development in
Neurospora crassa
Authors: Cea-Sánchez Sara , Martín-Villanueva Sara , Gutiérrez Gabriel , Cánovas David , Corrochano Luis M. 
Published: September 2024

ABSTRACT

Sexual reproduction in fungi allows genetic recombination and increases genetic diversity, allowing adaptation and survival. The velvet complex is a fungal-specific protein assembly that regulates development, pathogenesis, and secondary metabolism in response to environmental cues, such as light. In
Neurospora crassa
, this complex comprises VE-1, VE-2, and LAE-1. Deletion of
ve-1
or
ve-2
, but not
lae-1
, leads to increased conidiation (asexual spore formation) and reduced sexual development. Mutants lacking
ve-1
and/or
ve-2
are female sterile and male fertile, indicating that a VE-1/VE-2 complex regulates the development of female structures. During sexual development, we observed differential regulation of 2,117 genes in dark and 4,364 genes in light between the wild type and the ∆
ve-1
strain. The pheromone response and cell wall integrity pathways were downregulated in the ∆
ve-1
mutant, especially in light. Additionally, we found reduced levels of both total and phosphorylated MAK-1 and MAK-2 kinases.
In vitro
experiments demonstrated the binding of VE-1 and VE-2 to the promoters of
mak-1
and
mak-2
, suggesting a direct regulatory role of VE-1/VE-2 in the transcriptional control of MAPK genes to regulate sexual development. Deletion of the photosensor gene
white-collar 1
prevented the light-dependent inhibition of sexual development in the ∆
ve-1
mutant by increasing transcription of the pheromone response and cell wall integrity pathway genes to the levels in the dark. Our results support the proposal that the regulation of the MAP kinase pathways by the VE-1/VE-2 complex is a key element in transcriptional regulation that occurs during sexual development.

IMPORTANCE

Sexual reproduction generates new gene combinations and novel phenotypic traits and facilitates evolution. Induction of sexual development in fungi is often regulated by environmental conditions, such as the presence of light and nutrients. The velvet protein complex coordinates internal cues and environmental signals to regulate development. We have found that VE-1, a component of the velvet complex, regulates transcription during sexual development in the fungus
Neurospora crassa
. VE-1 regulates the transcription of many genes, including those involved in mitogen-activated protein kinase (MAPK) signaling pathways that are essential in the regulation of sexual development, and regulates the activity of the MAPK pathway. Our findings provide valuable insights into how fungi respond to environmental signals and integrate them into their reproductive processes.
Molecular and structural insights into SARS-CoV-2 evolution: from BA.2 to XBB subvariants
Authors: Yajima Hisano , Nomai Tomo , Okumura Kaho , Maenaka Katsumi ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Ito Jumpei , Hashiguchi Takao , Sato Kei , Matsuno Keita , Nao Naganori , Sawa Hirofumi , Mizuma Keita , Li Jingshu , Kida Izumi , Mimura Yume , Ohari Yuma , Tanaka Shinya , Tsuda Masumi , Wang Lei , Oda Yoshikata , Ferdous Zannatul , Shishido Kenji , Mohri Hiromi , Iida Miki , Fukuhara Takasuke , Tamura Tomokazu , Suzuki Rigel , Suzuki Saori , Tsujino Shuhei , Ito Hayato , Kaku Yu , Misawa Naoko , Plianchaisuk Arnon , Guo Ziyi , Hinay Alfredo A. , Usui Kaoru , Saikruang Wilaiporn , Lytras Spyridon , Uriu Keiya , Yoshimura Ryo , Kawakubo Shusuke , Nishumura Luca , Kosugi Yusuke , Fujita Shigeru , M.Tolentino Jarel Elgin , Chen Luo , Pan Lin , Li Wenye , Yo Maximilian Stanley , Horinaka Kio , Suganami Mai , Chiba Mika , Yasuda Kyoko , Iida Keiko , Strange Adam Patrick , Ohsumi Naomi , Tanaka Shiho , Ogawa Eiko , Fukuda Tsuki , Osujo Rina , Yoshimura Kazuhisa , Sadamas Kenji , Nagashima Mami , Asakura Hiroyuki , Yoshida Isao , Nakagawa So , Takayama Kazuo , Hashimoto Rina , Deguchi Sayaka , Watanabe Yukio , Nakata Yoshitaka , Futatsusako Hiroki , Sakamoto Ayaka , Yasuhara Naoko , Suzuki Tateki , Kimura Kanako , Sasaki Jiei , Nakajima Yukari , Irie Takashi , Kawabata Ryoko , Sasaki-Tabata Kaori , Ikeda Terumasa , Nasser Hesham , Shimizu Ryo , Begum Mst Monira , Jonathan Michael , Mugita Yuka , Leong Sharee , Takahashi Otowa , Ueno Takamasa , Motozono Chihiro , Toyoda Mako , Saito Akatsuki , Kosaka Anon , Kawano Miki , Matsubara Natsumi , Nishiuchi Tomoko , Zahradnik Jiri , Andrikopoulos Prokopios , Padilla-Blanco Miguel , Konar Aditi 
Published: September 2024

ABSTRACT

Due to the incessant emergence of various SARS-CoV-2 variants with enhanced fitness in the human population, controlling the COVID-19 pandemic has been challenging. Understanding how the virus enhances its fitness during a pandemic could offer valuable insights for more effective control of viral epidemics. In this manuscript, we review the evolution of SARS-CoV-2 from early 2022 to the end of 2023—from Omicron BA.2 to XBB descendants. Focusing on viral evolution during this period, we provide concrete examples that SARS-CoV-2 has increased its fitness by enhancing several functions of the spike (S) protein, including its binding affinity to the ACE2 receptor and its ability to evade humoral immunity. Furthermore, we explore how specific mutations modify these functions of the S protein through structural alterations. This review provides evolutionary, molecular, and structural insights into how SARS-CoV-2 has increased its fitness and repeatedly caused epidemic surges during the pandemic.
Complete genome sequence of antibiotic-producing
Streptomyces
sp. HBERC⁃20821, isolated from Wawushan Hill, Sichuan Province, China
Authors: Zhang Yifan , Wan Zhongyi , Chen Ling , Zhu Lei , Qiu Yimin , Chen Wei , Liu Xiaoyan , Min Yong 
Published: September 2024

ABSTRACT

The complete genome of a
Streptomyces
capable of producing multiple antibiotics was sequenced. Strain HBERC-20821 was isolated from a soil sample collected at Wawushan Hill, Sichuan Province, China. Genomic information will facilitate our systematic genetic manipulation of the strain at the gene level, enhancing its antibiotic production.
Draft genome sequence of
Bacillus velezensis
endophytically isolated from roots of
Polygala paniculata
Authors: de Paula Nogueira Cruz Felipe , Marques de Andrade Paulo Henrique , Paiva de Sousa Cristina , Teixeira Lacava Paulo 
Published: September 2024

ABSTRACT

Polygala paniculata
is a medicinal plant that harbors a remaining unknown microbiome. Those plants are known for their analgesic and anti-inflammatory properties and are widely found in the Brazilian Atlantic Forest. Herein, we report the isolation of the endophyte
Bacillus velezensis
GPP30 with a draft genome estimated at 4.0 Mpb.
Complete genome sequence of
Sphingobacterium multivorum
strain FW102 with β-galactosidase activity in drinking fountain water
Authors: Kim Sung Guk , Wang Sharon X. 
Published: September 2024

ABSTRACT

Sphingobacterium multivorum
is a ubiquitous environmental microbe in nature, particularly abundant in soil and water sources. Recently,
S. multivorum
has been considered to be a potential opportunistic pathogen in humans. We report the 5,9540,064-bp genome sequence of
S. multivorum
strain FW102
,
isolated from drinking fountain water and predicted to have multiple copies of β-galactosidase genes.
Necrotising enterocolitis suspicion in newborns with duct-dependent congenital heart disease: prognosis and risk factor
Authors: El Louali Fedoua , Prom Camille , Myriem Belghiti Alaoui , Gran Celia , Fouilloux Virginie , Lenoir Marien , Ligi Isabelle , Ovaert Caroline , Michel Fabrice 
Published: September 2024

IntroductionThe main risk factors of necrotising enterocolitis (NEC) are prematurity and low birth weight. The aim of our study was to identify risk factors for NEC in patients with duct-dependent congenital heart disease (CHD).Study designNewborns with duct-dependent CHD and NEC were matched 1:1 to those without NEC. Matched criteria were gestational age, birth weight, antenatal versus postnatal diagnosis and type of CHD.ResultsTwenty-three infants were included in each group. In the NEC group, mortality, length of intensive care unit stay and length of hospital stay were significantly higher (p=0.035; p<0.0001; p<0.0001). Lower diastolic blood pressure (DBP), negative flow balance, peritoneal dialysis and epinephrine-infusion were significantly associated with NEC (respectively, p=0.008, p=0.002, p=0.007, p=0.017). In multivariate analysis, DBP≤30 mm Hg remained the only independent risk factor of NEC (OR=8.70; 95% CI (1.46 to 53.50), p=0.019).ConclusionA DBP lower than 30 mm Hg was in our matched population of newborns with duct-dependent CHD, independently associated with NEC.
Metabolic reprogramming by mutant GNAS creates an actionable dependency in intraductal papillary mucinous neoplasms of the pancreas
Authors: Makino Yuki , Rajapakshe Kimal I , Chellakkan Selvanesan Benson , Okumura Takashi , Date Kenjiro , Dutta Prasanta , Abou-Elkacem Lotfi , Sagara Akiko , Min Jimin , Sans Marta , Yee Nathaniel , Siemann Megan J , Enriquez Jose , Smith Paytience , Bhattacharya Pratip , Kim Michael , Dede Merve , Hart Traver , Maitra Anirban , Thege Fredrik Ivar 
Published: September 2024

BackgroundOncogenic ‘hotspot’ mutations ofKRASandGNASare two major driver alterations in intraductal papillary mucinous neoplasms (IPMNs), which arebona fideprecursors to pancreatic ductal adenocarcinoma. We previously reported that pancreas-specificKrasG12DandGnasR201Cco-expression in p48Cre; KrasLSL-G12D; Rosa26LSL-rtTA; Tg (TetO-GnasR201C) mice (‘Kras;Gnas’ mice) caused development of cystic lesions recapitulating IPMNs.ObjectiveWe aim to unveil the consequences of mutantGnasR201Cexpression on phenotype, transcriptomic profile and genomic dependencies.DesignWe performed multimodal transcriptional profiling (bulk RNA sequencing, single-cell RNA sequencing and spatial transcriptomics) in the‘Kras;Gnas’ autochthonous model and tumour-derived cell lines (Kras;Gnascells), whereGnasR201Cexpression is inducible. A genome-wide CRISPR/Cas9 screen was conducted to identify potential vulnerabilities inKrasG12D;GnasR201Cco-expressing cells.ResultsInduction ofGnasR201C—and resulting G(s)alpha signalling—leads to the emergence of a gene signature of gastric (pyloric type) metaplasia in pancreatic neoplastic epithelial cells. CRISPR screening identified the synthetic essentiality of glycolysis-related genesGpi1andSlc2a1inKrasG12D;GnasR201Cco-expressing cells. Real-time metabolic analyses inKras;Gnascells and autochthonousKras;Gnasmodel confirmed enhanced glycolysis onGnasR201Cinduction. Induction ofGnasR201CmadeKrasG12Dexpressing cells more dependent on glycolysis for their survival. Protein kinase A-dependent phosphorylation of the glycolytic intermediate enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) was a driver of increased glycolysis onGnasR201Cinduction.ConclusionMultiple orthogonal approaches demonstrate thatKrasG12DandGnasR201Cco-expression results in a gene signature of gastric pyloric metaplasia and glycolytic dependency during IPMN pathogenesis. The observed metabolic reprogramming may provide a potential target for therapeutics and interception of IPMNs.
Access Characteristic-Guided Remote Swapping Across Mobile Devices
Authors: Li Wentong , Lv Yina , Luo Longfei , Song Yunpeng , Shi Liang 
Published: September 2024

Memory swapping ensures smooth application switching for mobile systems by caching applications in the background. To further play the role of memory swapping, remote swapping across mobile devices has been widely studied, which caches applications to nearby remote devices by remote paging. However, due to the massive remote I/Os and unguaranteed swap throughput, the current remote swapping is limited with an unsatisfactory user experience, especially under variable network conditions. This paper first studies the access characteristics of applications and clarifies the impact of various network traffic on remote swapping. Motivated by these, an efficient access characteristic-guided remote swapping framework (ACR-Swap
+
) is proposed to optimize remote swapping across mobile devices with resilient remote paging. ACR-Swap
+
first performs selective remote paging based on the swap-in frequency of different processes and then prefetches data across devices based on the process running states. Finally, it conducts hierarchical remote paging to avoid the impact of network traffic on remote swapping. Evaluations on Google Pixel 6 show that ACR-Swap
+
reduces the application switching latency by 21.6% and achieves a negligible performance fluctuation under various network traffic compared to the state of the art.
Nutrient Levels and Nutrient Sources in Pancreatic Tumors
Authors: Groessl Sven , Palm Wilhelm 
Published: September 2024

Abstract
It has been known that poor tumor perfusion and dysregulated cancer cell metabolism give rise to tumor microenvironments with unphysiologic nutrient levels, but the precise alterations in metabolite abundance are not well defined. In a 2015 study in Cancer Research, Kamphorst and colleagues published a detailed comparison of the metabolome from human pancreatic tumors and benign tissues. Tumors were depleted in glucose and various nonessential amino acids but, surprisingly, enriched in essential amino acids. The authors attributed these nutrient imbalances to macropinocytosis of extracellular proteins, a RAS-driven amino acid acquisition pathway that was found to be increased in human tumors and supports pancreatic cancer cell growth during amino acid starvation. These findings substantially contributed to the understanding of altered nutrient levels in tumors and extracellular proteins as noncanonical nutrients. Intratumoral nutrient levels in different cancer contexts and signaling pathways that regulate nutrient acquisition by cancer cells remain a focus of current research.
See related article by Kamphorst and colleagues, Cancer Res 2015;75:544–53
Cancer-Associated Fibroblasts: From Spectators to Protagonists in Pancreatic Cancer Progression
Authors: Mucciolo Gianluca , Li Wenlong , Biffi Giulia 
Published: September 2024

Abstract
Our knowledge of the origins, heterogeneity, and functions of cancer-associated fibroblasts (CAF) in pancreatic ductal adenocarcinoma (PDAC) has exponentially increased over the last two decades. This has been facilitated by the implementation of new models and single-cell technologies. However, a few key studies preceded the current exciting times in CAF research and were fundamental in initiating the investigation of CAFs and of their roles in PDAC. With their study published in Cancer Research in 2008, Hwang and colleagues have been first to successfully isolate and immortalize human pancreatic stellate cells (HPSC) from PDAC tissues. This new tool allowed them to probe the roles of CAFs in PDAC as never done before. By performing complementary in vitro and in vivo analyses, the authors demonstrated the involvement of HPSCs in PDAC malignant cell proliferation, invasion, and therapy resistance. Here, we leverage that seminal study as a framework to discuss the advances made over the last 16 years in understanding the complexity and central roles of CAFs in PDAC progression.
See related article by Hwang and colleagues, Cancer Res 2008;68:918–26