bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bounding the localized to ductile transition in porous rocks: implications for geo-reservoirs
Authors: Meyer Gabriel G , Violay Marie 
Published: September 2023

SUMMARY
Porous rocks have long been the focus of intense research driven by their importance in our society as host to our most essential resources (oil, gas, water, geothermal energy, etc), yet their rheology remains poorly understood. With increasing depth, porous rocks transition from being brittle (dilational deformation leading to localized failure) to being ductile (homogeneous compactive flow, no failure). The transition between these two regimes is crucial for reservoir engineering. In fact, brittle, localized deformation of porous rocks is generally accompanied by permeability enhancement but also induced seismicity, while ductile deformation leads to aseismic permeability reduction. Decades of experimental work has shown that this transition is not sharp but rather spans a wide P, T domain, but to this day, no clear boundaries have been established. Here, we subjected pre-faulted samples of Volvic trachyandesite to increasing confining pressure, deforming the samples each pressure step and recording strain partitioning between off-fault bulk deformation and on-fault slip. For the first time, we show that the localized–ductile transition (LDT) in porous rocks is bound by the stress criterion σy &lt; σf &lt; σflow. Additionally we show that, in this regime, once both fault sliding and bulk flow are active, the partitioning of strain between the two can be described by the empirical ratio: $(\sigma _\mathrm{f}-\sigma _\mathrm{y})/(\sigma _\mathrm{flow}-\sigma _\mathrm{y}).$ Finally, we propose a critical stress representation that takes into account the existence of the LDT in porous rocks.
Outcome of Very Early Onset Inflammatory Bowel Disease Associated With Primary Sclerosing Cholangitis: A Multicenter Study From the Pediatric IBD Porto Group of ESPGHAN
Authors: Catassi Giulia , D’Arcangelo Giulia , Norsa Lorenzo , Bramuzzo Matteo , Hojsak Iva , Kolho Kaija-Leena , Romano Claudio , Gasparetto Marco , Di Giorgio Angelo , Hussey Seamus , Yerushalmy-Feler Anat , Turner Dan , Matar Manar , Weiss Batia , Karoliny Anna , Alvisi Patrizia , Tzivinikos Christos , Aloi Marina 
Published: September 2023

Abstract

Background
Whether primary sclerosing cholangitis related to inflammatory bowel disease (PSC-IBD) diagnosed before 6 years (ie, VEO-IBD) has a distinct phenotype and disease course is uninvestigated. We aimed to analyze the characteristics and natural history of VEO-PSC-IBD, compared with early and adolescent-onset PSC-IBD.

Methods
This is a multicenter, retrospective, case-control study from 15 centers affiliated with the Porto and Interest IBD group of ESPGHAN. Demographic, clinical, laboratory, endoscopic, and imaging data were collected at baseline and every 6 months. Inflammatory bowel disease–related (clinical remission, need for systemic steroids and biologics, and surgery) and PSC-related (biliary and portal hypertensive complications, need for treatment escalation and liver transplantation, cholangiocarcinoma, or death) outcomes were compared between the 2 groups.

Results
Sixty-nine children were included, with a median follow-up of 3.63 years (interquartile range, 1-11): 28 with VEO-PSC-IBD (23 UC [82%], 2 IBD-U [7%] and 3 [11%] CD), and 41 with PSC-IBD (37 UC [90%], 3 IBDU [7.5%] and 1 [2.5%] CD). Most patients with UC presented with pancolitis (92% in VEO-PSC-UC vs 85% in PSC-UC, P = .2). A higher number of patients with VEO-PSC-IBD were diagnosed with PSC/autoimmune hepatitis overlap syndrome than older children (24 [92%] vs 27 [67.5%] PSC-IBD, P = .03), whereas no other differences were found for PSC-related variables. Time to biliary strictures and infective cholangitis was lower in the VEO-PSC-IBD group (P = .01 and P = .04, respectively), while no difference was found for other outcomes. No cases of cholangiocarcinoma were reported.

Conclusions
Primary sclerosing cholangitis related to inflammatory bowel disease has similar baseline characteristics whether diagnosed as VEO-IBD or thereafter. A milder disease course in terms of biliary complications characterizes VEO-PSC-IBD.
Income growth, forecasting and stock valuation
Authors: Psychoyios Dimitris 
Published: September 2023

Abstract
Accepted by: Aris Syntetos
We show that using forecasts of a firm’s income growth in the context of stock valuation can lead to overpricing of the firm’s stock, which is consistent with ‘optimism bias’ reported among financial analysts. Firms with volatile earnings, high income growth and low systematic risk are prone to larger valuation errors. To address this issue, we develop a new estimator of the firm value that corrects for the bias from forecasting income growth. The new estimator is significantly superior to the traditional value estimator under various performance measures. To support managerial decision-making, we construct closed-form confidence intervals for the firm value and the implied cost of capital that account for uncertainty in income growth.
The Higher Structure of Unstable Homotopy Groups
Authors: Basu Samik , Blanc David , Sen Debasis 
Published: September 2023

Abstract
We construct certain unstable higher order homotopy operations indexed by the simplex categories of $\boldsymbol{\Delta }^{n}$ for $n\geq 2$, and prove that all elements in the homotopy groups of a wedge of spheres are generated under such operations by Whitehead products and the group structure. This provides a stronger unstable analogue of Cohen’s theorem on the decomposition of stable homotopy.
Genomic Epidemiology of Treponema pallidum and Circulation of Strains With Diminished tprK Antigen Variation Capability in Seattle, 2021–2022
Authors: Lieberman Nicole A P , Avendaño Carlos C , Bakhash Shah A K Mohamed , Nunley Ethan , Xie Hong , Giacani Lorenzo , Berzkalns Anna , Soge Olusegun O , Reid Tara B , Golden Matthew R , Greninger Alexander L 
Published: September 2023

Abstract

Background
The incidence of syphilis continues to increase in the United States, yet little is known about Treponema pallidum genomic epidemiology within American metropolitan areas.

Methods
We performed whole-genome sequencing and tprK deep sequencing of 28 T. pallidum–containing specimens, collected mostly from remnant Aptima swab specimens from 24 individuals from Seattle Sexual Health Clinic during 2021–2022.

Results
All 12 individuals infected with Nichols-lineage strains were men who have sex with men, while a specific SS14 cluster (mean, 0.33 single-nucleotide variant) included 1 man who has sex with women and 5 women. All T. pallidum strains sequenced were azithromycin resistant via 23S ribosomal RNA A2058G mutation. Identical T. pallidum genomic sequences were found in pharyngeal and rectal swab specimens taken concurrently from the same individuals. The tprK sequences were less variable between patient-matched specimens and between epidemiologically linked clusters. We detected a 528–base pair deletion in the tprK donor site locus, eliminating 9 donor sites, in T. pallidum genomes of 3 individuals with secondary syphilis, associated with diminution of TprK diversity.

Conclusions
We developed an end-to-end workflow for public health genomic surveillance of T. pallidum from remnant Aptima swab specimens. tprK sequencing may assist in linking cases beyond routine T. pallidum genome sequencing. T. pallidum strains with deletions in tprK donor sites currently circulate and are associated with diminished TprK antigenic diversity.
Environmental Surveillance for Salmonella Typhi and its Association With Typhoid Fever Incidence in India and Malawi
Authors: Uzzell Christopher B , Abraham Dilip , Rigby Jonathan , Troman Catherine M , Nair Satheesh , Elviss Nicola , Kathiresan Lalithambigai , Srinivasan Rajan , Balaji Veeraraghavan , Zhou Nicolette A , Meschke John Scott , John Jacob , Kang Gagandeep , Feasey Nicholas , Mohan Venkata Raghava , Grassly Nicholas C 
Published: September 2023

Abstract

Background
Environmental surveillance (ES) for Salmonella Typhi potentially offers a low-cost tool to identify communities with a high burden of typhoid fever.

Methods
We developed standardized protocols for typhoid ES, including sampling site selection, validation, characterization; grab or trap sample collection, concentration; and quantitative PCR targeting Salmonella genes (ttr, staG, and tviB) and a marker of human fecal contamination (HF183). ES was implemented over 12 months in a historically high typhoid fever incidence setting (Vellore, India) and a lower incidence setting (Blantyre, Malawi) during 2021–2022.

Results
S. Typhi prevalence in ES samples was higher in Vellore compared with Blantyre; 39/520 (7.5%; 95% confidence interval [CI], 4.4%–12.4%) vs 11/533 (2.1%; 95% CI, 1.1%–4.0%) in grab and 79/517 (15.3%; 95% CI, 9.8%–23.0%) vs 23/594 (3.9%; 95% CI, 1.9%–7.9%) in trap samples. Detection was clustered by ES site and correlated with site catchment population in Vellore but not Blantyre. Incidence of culture-confirmed typhoid in local hospitals was low during the study and zero some months in Vellore despite S. Typhi detection in ES.

Conclusions
ES describes the prevalence and distribution of S. Typhi even in the absence of typhoid cases and could inform vaccine introduction. Expanded implementation and comparison with clinical and serological surveillance will further establish its public health utility.
Epigenetic effects of ceftriaxone-resistant Neisseria gonorrhoeae FC428 mosaic-like sequences found in PenA sequences unique to Neisseria subflava and related species
Authors: Kanesaka Izumo , Ohno Akira , Morita Masahiro , Katsuse Akiko Kanayama , Morihana Takefumi , Ito Takamitsu , Takahashi Hiroshi , Kobayashi Intetsu 
Published: September 2023

Abstract

Objectives
The aim of this study was to explore the origin of the PenA mosaic amino acid sequence in the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone.

Methods
The penA sequences of 27 Neisseria subflava pharyngeal isolates were determined by the Sanger method and penA sequences of 52 isolates from nine Neisseria species were obtained from the NCBI database. Comparative analysis of each PenA sequence was performed by multiple sequence alignment using ClustalW.
In vitro resistance acquisition experiments were conducted to investigate the possibility of selection pressure by cefixime-induced amino acid substitution mutations in PenA.

Results
All N. subflava strains, including two with low susceptibility to expanded-spectrum cephalosporins (ESCs), possessed the majority of the PenA FC428 sequence. Furthermore, a number of strains, but not all, of closely related species of N. subflava showed similar results. PenA FC428 sequences were also found in some strains of distantly related species. No new mutations in the penA sequence were observed in colonies with increased MIC in in vitro resistance acquisition experiments.

Conclusions
This study provides strong evidence that the FC428 PenA mosaic sequence originated from N. subflava and related species among oral commensal Neisseria species. The results of in vitro resistance acquisition experiments also suggested that one of the PenA FC428-like sequence gene polymorphisms resulted in the expression of ESC resistance. Furthermore, many of the PenA FC428 mosaic sequences were thought to be involved in the so-called epistasis effect that regulates the expression of resistance, without directly contributing to the resistance level itself.
Impact of pretreatment low-abundance HIV-1 drug resistance on virological failure after 1 year of antiretroviral therapy in China
Authors: Li Miaomiao , Song Chang , Hu Jing , Dong Aobo , Kang Ruihua , Feng Yi , Xing Hui , Ruan Yuhua , Shao Yiming , Hong Kunxue , Liao Lingjie 
Published: September 2023

Abstract

Objectives
To assess the impact of pretreatment low-abundance HIV drug-resistant variants (LA-DRVs) on virological outcomes among ART-naive HIV-1-infected Chinese people who initiated ART.

Methods
A nested case–control study was conducted among HIV-1-infected individuals who had pretreatment drug resistance (PDR) genotypic results. Cases were defined as individuals with virological failure (HIV-1 RNA viral load ≥1000 copies/mL) after 1 year of ART, and controls were individuals from the same cohort whose viral load was less than 1000 copies/mL. Next-generation sequencing was used to identify low-abundance PDR mutations at detection thresholds of 10%, 2% and 1%. The mutant load was calculated by multiplying the abundance of HIV-1 drug-resistant variants by the pretreatment viral load. The impact of pretreatment low-abundance mutations on virological failure was estimated in logistic regression models.

Results
Participants (43 cases and 100 controls) were included in this study for the analysis. The proportion of participants with PDR was higher in cases than in controls at different detection thresholds (44.2% versus 22.0%, P = 0.007 at 10% threshold; 58.1% versus 31.0%, P = 0.002 at 2% threshold; 90.7% versus 69.0%, P = 0.006 at 1% threshold). Compared with participants without PDR, participants with ≥10% detectable PDR mutations were associated with an increased risk of virological failure (adjusted OR 8.0, 95% CI 2.4–26.3, P = 0.001). Besides this, individuals with pretreatment LA-DRVs (2%–9% abundance range) had 5-fold higher odds of virological failure (adjusted OR 5.0, 95% CI 1.3–19.6, P = 0.021). Furthermore, LA-DRVs at 2%–9% abundance resistant to NRTIs and mutants with abundance of ≥10% resistant to NNRTIs had a 4-fold and 8-fold risk of experiencing virological failure, respectively. It was also found that a mutant load of more than 1000 copies/mL was predictive of virological failure (adjusted OR 7.2, 95% CI 2.5–21.1, P = 0.0003).

Conclusions
Low-abundance PDR mutations ranging from 2% to 9% of abundance can increase the risk of virological failure. Further studies are warranted to define a clinically relevant threshold of LA-DRVs and the role of NRTI LA-DRVs.
Determination of Tilmicosin in Bovine, Swine, Chicken, and Turkey Tissues by Liquid Chromatography With Tandem Mass Spectrometry, Single-Laboratory Validation
Authors: Rodewald John Matt , Burnett Thomas J , Brunelle Sharon L , Ward Clive , Coleman Mark R 
Published: September 2023

Abstract

Background
An LC-MS/MS method was developed for determination and confirmation of tilmicosin in bovine, swine, chicken, and turkey tissues (liver, kidney, muscle, and skin/fat) and bovine milk.

Objective
The method was subjected to single-laboratory validation to establish method performance parameters.

Method
Animal tissues and bovine milk were fortified at four concentrations ranging from 0.5 times the lowest maximum residue limit (MRL) or tolerance to 2 times the highest MRL or tolerance considering the Codex and EU MRLs and the US tolerances in the various tissues and milk studied. Incurred tissues were analyzed to verify the precision of the method.

Results
The data demonstrated linearity of matrix-matched calibration curves using a weighted (1/×) regression. Recoveries varied from 83.3 to 107.1%. Repeatability precision (RSDr) ranged from 0.465 to 13.4% and intermediate precision (RSDi) ranged from 2.24 to 14.7% in fortified tissue. Repeatability of the method was verified in incurred tissues, ranging from 3.41 to 16.0%. The limits of detection and quantitation of the method are presented and vary by matrix. One confirmatory transition ion was examined across all matrixes and met US and EU criteria for mass spectrometry confirmation. The method was shown to be robust when small changes in method parameters were made, and stability of the analyte in fortified tissues, extracts, standard solutions, and matrix-matched standards was estimated.

Conclusions
The data satisfy the requirements of the AOAC Stakeholder Panel for Veterinary Drug Residue Methods for single-laboratory validation studies and the U.S. Food and Drug Administration Center for Veterinary Medicine Guidance for Industry #208 (VICH GL49).

Highlights
The LC-MS/MS method was demonstrated to be suitable for determination and confirmation of tilmicosin residues in bovine, swine, chicken, and turkey tissues and bovine milk based on Codex and EU MRLs and US tolerances.
Ecological succession of blow flies (Diptera: Calliphoridae) in the decomposition of pig carcasses in Cerrado areas of Brazil
Authors: Silva José Orlando de Almeida , Carvalho-Filho Fernando da Silva , Juen Leandro , Esposito Maria Cristina 
Published: September 2023

AbstractThis research aims to describe the process of ecological succession by associating the decomposition stages of pig carcasses with flies from the Calliphoridae family (Diptera). For this, 6 pig carcasses were exposed in Maranhão’s Cerrado, utilizing metal cages with sawdust trays to catch immature specimens and “suspended traps” to capture adults. Adults of the Hemilucilia benoisti Séguy, and Hemilucilia townsendi Shannon species were only associated with the swelling stage. Chrysomya megacephala (Fabricius) was associated with 2 stages (black putrefaction and fermentation). The species Chloroprocta idioidea (Robineau-Desvoidy), Chrysomya albiceps (Wiedemann), Cochliomyia macellaria (Fabricius), and Lucilia eximia (Wiedemann) were associated with 4 of the 5 stages of decomposition, the latter being the only 1 associated with the initial stage. The larvae abandoned the carcasses to pupate from the second stage of decomposition, with L. eximia being the only 1 leaving the carcasses in the swelling stage, and C. albiceps the only 1 associated with both the fermentation and dry stages. Our findings indicate that calliphorid species can help forensic investigators estimine the post-mortem interval of cadavers in situations similar to those detailed in this study. Since there was a link between adult and immature species and certain stages, they can be used as indicators in future forensic investigations.
Climatic factors regulate the assembly processes of abundant and rare microbial communities in desert soil
Authors: Sun Qiang , Li Hang-Yu , Li Kuan , Zhang Xiao-Qing , Shi Ya-Bo , Wu Yan-Tao , Li Xing , Li Zhi-Yong , Zhang Jing-Hui , Wang Li-Xin , Liang Cun-Zhu 
Published: September 2023

Abstract
Soil microorganisms, which include many rare taxa and a small number of abundant taxa, have different contributions to the ecosystem functions and services. High throughput sequencing technology was used to analyze the species composition of soil samples by DNA sequencing. Soil microorganisms were divided into abundant taxa and rare taxa to reveal their composition. Correlation analysis and random forest method were used to further analyze the influence of environmental factors on the community. Finally, the beta nearest taxon index (βNTI) based on the null model was used to elucidate the mechanisms underlying soil microbial community assembly. We found that, in desert soil, the community assembly of rare bacteria was almost entirely dominated by a homogeneous selection of deterministic processes. For comparison, stochastic processes had more pronounced effects on the abundant bacteria. However, both abundant and rare fungi exhibited similar patterns of community assembly, i.e. deterministic and stochastic processes jointly determined the assembly processes of fungal communities. We also observed that community assembly shifted from stochastic to deterministic processes with increasing mean annual precipitation (MAP) and mean annual temperature (MAT) for abundant bacteria. Conversely, for rare fungi, there was an inclination toward a shift from deterministic to stochastic processes with rising MAT. In conclusion, our findings provide compelling evidence that MAT and MAP regulate the community assembly process of abundant and rare microbial communities in desert soil. These findings establish a theoretical foundation for future investigations into the community structure and ecological functions of soil microorganisms.
Intimacy and survivors of cancer with ostomies: findings from the Ostomy Self-management Training trial
Authors: Nehemiah Ariel , Zhang Siqi , Appel Scott , Dizon Don , Sun Virginia , Grant Marcia , Holcomb Michael J , Hornbrook Mark C , Krouse Robert S 
Published: September 2023

Abstract

Background
Many people with abdominal or pelvic cancers require an ostomy during surgical treatment, which can cause significant issues with physical and emotional intimacy in relationships.

Aim
To evaluate the effect of a telehealth-based education program on intimacy over time for survivors of cancer with ostomies.

Methods
We performed a secondary analysis of our multicenter randomized controlled trial to determine intimacy outcomes and to compare the effects of the Ostomy Self-management Training (OSMT) program vs usual care. Partnered patients were included who provided answers to the City of Hope Quality of Life–Ostomy survey for at least 2 time points during the study. We evaluated the effect of baseline information, such as gender on intimacy.

Outcomes
The primary outcome was intimacy, estimated by a composite score created from questions within the City of Hope Quality of Life–Ostomy survey.

Results
Of 216 enrolled volunteers, 131 had a partner: 68 in the OSMT arm and 63 in the usual care arm. Of these, 48 were women and 83 were men. The tumor types represented in this study were colorectal (n = 69), urinary (n = 45), gynecologic (n = 10), and other (n = 7; eg, melanoma, liposarcoma). From the cohort, 87 answered the 5 composite intimacy score questions at 2 time points, including baseline. There was significant improvement over time in composite intimacy scores for participants in the OSMT arm vs the usual care arm.

Clinical Implications
Our OSMT intervention had a positive effect on factors that contribute to intimacy for survivors of cancer with ostomies, suggesting that a survivorship curriculum can improve their experiences after ostomy surgery.

Strengths and Limitations
OSMT allowed for discussion of intimacy and other sensitive topics, which can be challenging. These discussions demonstrate benefit to participants and can serve as frameworks for cancer treatment providers. The focus of this work on partnered participants provides insight into the interpersonal challenges of a life with an ostomy, but it may overlook the important perspectives of nonpartnered participants and the partners themselves. Furthermore, limited power prevented us from conducting subgroup analyses exploring the effects of factors such as gender and tumor type on intimacy.

Conclusion
At 6-month follow-up, the novel intimacy composite score indicated improvement for participants completing the OSMT intervention. Future research studies with higher power will validate this intimacy measurement and identify intimacy differences in similar populations based on tumor type.
‘Transforming our world’? A historical materialist critique of the sustainable development agenda
Authors: Leichtweis Matheus Gobbato 
Published: September 2023

Abstract
Questioning the transformative potential of the Sustainable Development Goals, the article mobilises elements of critical theory in order to demonstrate how contemporary forms of global sustainability governance refrain from tackling the capitalist roots of unsustainable development. For this reason, they remain incapable of delivering on their promises of world transformation.