bluuebunny/crossref_metadata_2025_split huggingface dataset:
Locked down in distress: A quasi‐experimental estimation of the mental‐health fallout from the COVID‐19 pandemic
Authors: Anaya Lina , Howley Peter , Waqas Muhammad , Yalonetzky Gaston 
Published: October 2023

AbstractWe use a large‐scale longitudinal survey with a differences‐in‐differences research design to estimate the impact of the COVID‐19 pandemic on mental health in the United Kingdom. We report substantial increases in psychological distress for the population overall during the first wave. These impacts were not uniformly distributed, with the mental health costs being more pronounced for females, younger cohorts, the black, Asian and minority ethnic community, and migrants. We also identified characteristics capable of predicting resilience to the mental health effects. We find that people with financial worries, loneliness or living in overcrowded dwellings experienced significantly worse mental health deterioration during the first wave.
Risk‐averse two‐stage stochastic programming for the inventory rebalancing of bike‐sharing systems
Authors: Walker Awnalisa , Kwon Soongeol 
Published: October 2023

AbstractAs the popularity and usage of bike‐sharing systems increase, a better decision‐making model tailored for the successful operations of bike‐sharing systems is needed. This study is motivated to address operator‐based inventory rebalancing of bike‐sharing systems, and the main objective is to develop a mathematical optimization model designed to derive an optimal daily inventory rebalancing plan. Specifically, this study proposes a risk‐averse two‐stage stochastic programming to determine optimal initial inventory levels for each station to minimize operational costs for relocating bikes and expected penalty costs due to unmet requests. This study adopts the conditional value at risk to properly measure the risk associated with unmet requests to implement risk‐averse stochastic programming. Numerical experiments are conducted based on scenario data generated by empirical distributions fitted to trip data from the Houston BCycle to validate and evaluate the proposed model. The results show that the proposed model can be successfully applied to inventory rebalancing to improve the usability of bike‐sharing systems.
The information spillover role of corporate spin‐offs in financing activities: Evidence from equity sales by private firms through Regulation D
Authors: Kim Sangwan , Suh Jangwon 
Published: October 2023

AbstractWe examine whether the increased quantity of public information has a spillover impact on equity sales by private industry peer firms. To capture an increase in the quantity of public peer information, we use corporate spin‐offs as these events cause an increase in the number of independent public entities that mandatorily disclose financial reports. Using a unique dataset on private firms’ equity sales extracted from the Securities and Exchange Commission filings pursuant to Regulation D, we find that private industry peers sell more equity following spin‐offs, but the increase is not statistically significant. When we divide our spin‐off sample based on the availability of segment information on subsidiaries before spin‐offs, however, we find a significant an increase in private firms’ equity sales after spin‐offs when parent firms did not previously disclose segment reports. Additional test results suggest that our inferences regarding private industry peers are not entirely explained by an industry‐wide demand shock. Overall, we contribute to the literature by establishing an information spillover channel, incremental to the effect of common industry shocks, flowing from the public to private markets.
A protocol for creating endometriosis in rhesus macaques (Macaca mulatta)
Authors: Slayden Ov D. , Luo Fangzhou , Martin, D.V.M Lauren D. 
Published: October 2023

AbstractBackgroundEndometriosis is the presence of endometrium‐like tissue outside the uterine cavity. An experimental model of endometriosis has been created in the baboon by the transcervical collection and laparoscopic inoculation of menstrual endometrium. Macaques are the preferred model for pharmaceutical development, but the complex anatomy of the macaque cervix makes the baboon method impractical. In this work, we sought to validate a surgical approach for creating endometriosis in macaques.MethodsMenstrual endometrium was collected via laparoscopic intrauterine puncture and transferred to the peritoneal cavity. We repeated this procedure during three menstruations. Endometriotic tissue was identified during laparoscopy, collected, and characterized by immunohistochemistry.ResultsSham surgery‐treated animals (n = 3) failed to develop endometriosis. We identified red, powder burnt, and white lesions in 13/14 of the treated animals; the stroma of the red lesions stained positive for ovarian steroid receptors.ConclusionThis surgical technique can reliably create hormone‐responsive endometriosis in macaques for therapeutic studies.
Idiopathic and structural episodic nonintentional head tremor in dogs: 100 cases (2004‐2022)
Authors: Liatis Theofanis , Bhatti Sofie F. M. , Dyrka Magdalena , Gutierrez‐Quintana Rodrigo , Gonçalves Rita , Madden Megan , De Decker Steven 
Published: October 2023

AbstractBackgroundAlthough idiopathic episodic head tremor (IEHT) in dogs is well‐known, little is known about structural brain lesions causing structural episodic head tremor (SEHT).Hypothesis/ObjectivesDescribe semiology, magnetic resonance imaging (MRI) findings and outcome of dogs with IEHT or SEHT. We hypothesized that structural lesions affecting the middle cranial fossa or mesencephalic aqueduct could lead to SEHT.AnimalsOne hundred dogs with IEHT (n = 71) or SEHT (n = 29).MethodsRetrospective, multicenter, study of dogs with episodic (nonintentional) head tremor and brain MRI between 2004 and 2022.ResultsLesions on MRI in SEHT dogs were localized to the middle cranial fossa (15/29), cerebrocortex (3/29), brainstem (2/29), fourth ventricle (1/29) or multifocal (8/29) with thalamus involvement (6/8). Secondary compression of the mesencephalic aqueduct (19/29), third ventricle or interthalamic adhesion or both (14/29) was common. The most common underlying condition in dogs with SEHT was a pituitary mass. Dogs with SEHT were older, had additional neurological signs and were more likely to be euthanized after diagnosis (P < .001 for all) compared to IEHT dogs. Two SEHT dogs had only tremor. In IEHT dogs, 8/10 owners reported that the tremor decreased or abated over time (range, 106‐2315 days) without treatment. Tremor remission occurred in SEHT dogs treated for underlying meningoencephalitis.Conclusions and Clinical ImportancePresence of additional neurological signs and older age may indicate an underlying structural cause for episodic (nonintentional) head tremor involving the mesencephalic aqueduct, third ventricle, interthalamic adhesion or some combination of these. An intracranial structural abnormality cannot be excluded in dogs with normal neurological examination.
R‐loops act as regulatory switches modulating transcription of COLD‐responsive genes in rice
Authors: He Zexue , Li Mengqi , Pan Xiucai , Peng Yulian , Shi Yining , Han Qi , Shi Manli , She Linwei , Borovskii Gennadii , Chen Xiaojun , Gu Xiaofeng , Cheng Xuejiao , Zhang Wenli 
Published: October 2023

Summary
COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R‐loops function in various cellular processes, including development and stress responses, in plants. However, how R‐loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.).
We conducted DRIP‐Seq along with other omics data (RNA‐Seq, DNase‐Seq and ChIP‐Seq) in rice with or without COLD treatment.
COLD treatment caused R‐loop reprogramming across the genome. COLD‐biased R‐loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R‐loops can directly/indirectly modulate the transcription of a subset of COLD‐responsive genes, which can be mediated by R‐loop overlapping TF‐centered or cis‐regulatory element‐related regulatory networks and lncRNAs, accounting for c. 60% of COLD‐induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R‐loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD‐responsive gene expression, as potential targets for enhanced COLD resistance.
Our study provides detailed evidence showing functions of R‐loop reprogramming during COLD responses and provides some potential R‐loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.
New liguleless (lg2) maize stocks: Genetic resources for leaf architectural and haploid induction rate assessment studies
Authors: Khulbe R. K. , Pattanayak A. , Sharma Devender , Bisht G. S. , Pant M. C. 
Published: October 2023

AbstractLiguleless mutants produce defective ligules and auricles and, consequently, have more upright leaves than their ligulate counterparts, making them useful genetic material for plant architectural studies. Besides, owing to the recessive nature and amenability of the liguleless trait to phenotyping at the seedling stage, liguleless mutants are popularly used for ‘proof‐of‐concept’ demonstration and assessment of haploid induction rate (HIR) of haploid inducer lines (HILs) in maize. The commonly used liguleless testers in maize are of temperate origin and are challenging to use and maintain under tropical/sub‐tropical conditions. In the present study, liguleless lines (V 601, V 602, V 603 and V 604) derived from crosses between agronomically superior locally adapted tropical ligulate lines (V 407 and CM 152) and liguleless donors of temperate origin (PDH‐3 and PDH‐8) were evaluated for different agro‐morphological traits. Liguleless line V 602 was also used as a tester to assess the HIR of haploid inducer line EC937890 (CIM2GTAILP2). The results showed a mean HIR of 12.42% for EC937890, consistent with the HIR reported in other studies, thus demonstrating the efficacy of V 602 as a tester for determining HIR. The agronomically superior liguleless maize lines reported in this study will, therefore, be a valuable resource for leaf architectural studies, assessment of HIR of candidate HILs and maintenance of high HIR in the HILs presently in wide use in the doubled haploid (DH) programmes. Additionally, these genetic stocks carry the liguleless trait in genetic backgrounds with known heterotic affinity with early maturity Indian public maize germplasm and, therefore, can be used directly as parents in hybrid development programmes.
The effect of an organ procurement organization surgeon on pediatric organ utilization
Authors: Hwang Christine S. , Shubin Andrew D. , Patel Madhukar S. , Reese Jeffrey C. , Sanchez‐Vivaldi Jorge A. , Desai Dev M. , Vagefi Parsia A. , MacConmara Malcolm 
Published: October 2023

AbstractIntroductionOrgan procurement organizations (OPO) have started to employ transplant‐trained surgeons dedicated to organ procurement with the aim to increase allograft utilization and enhance the use of procured organs. We investigated the effects of an OPO‐employed surgeon on the procurement and utilization of organs from pediatric donors within the Southwestern Transplant Alliance OPO.MethodsOPO data were obtained for all procurements that were performed between 2014 and 2019. The analysis was performed to see if the presence of an OPO donor surgeon impacted the utilization of pediatric livers. Donor and recipient demographic data were examined between allografts procured with the presence of an OPO surgeon (OPO‐Present) and those without an OPO surgeon (OPO‐Absent). A p‐value of <.05 was considered significant.ResultsOf 149 pediatric procurements, 91 included an OPO‐donor surgeon. In procurements with OPO‐Present, donors were younger (8.2 vs. 11.2, p < .05) and had longer distances to travel to the recipient center (334 vs. 175 miles p < .05), but had comparable cold ischemic times. In terms of organ share type, more OPO‐Present livers were shared nationally and there was no difference in discard rate between OPO‐Present and OPO‐Absent procurements. Finally, OPO‐Present livers were more likely to be transplanted to pediatric recipients compared to OPO‐Absent (47.3% vs. 24.1% p < .05).ConclusionThe presence of an OPO surgeon has impacted organ utilization, leading to increased transplantation of pediatric livers in pediatric recipients, and has expanded the geographical share of pediatric livers.
Timely estimation of leaf chlorophyll fluorescence parameters under varying light regimes by coupling light drivers to leaf traits
Authors: Song Guangman , Wang Quan , Zhuang Jie , Jin Jia 
Published: October 2023

AbstractUnveiling informative chlorophyll a fluorescence (ChlF) parameters and leaf morphological/biochemical traits under varying light conditions is important in ecological studies but has less been investigated. In this study, the trait‐ChlF relationship and regressive estimation of ChlF parameters from leaf traits under varying light conditions were investigated using a dataset of synchronous measurements of ChlF parameters and leaf morphological/biochemical traits in Mangifera indica L. The results showed that the relationships between ChlF parameters and leaf traits varied across light intensities, as indicated by different slopes and intercepts, highlighting the limitations of using leaf traits alone to capture the dynamics of ChlF parameters. Light drivers, on the other hand, showed a better predictive ability for light‐dependent ChlF parameters compared to leaf traits, with light intensity having a large effect on light‐dependent ChlF parameters. Furthermore, the responses of ФF and NPQ to light drivers differed between leaf types, with light intensity having an effect on ФF in shaded leaves, whereas it had a primary effect on NPQ in sunlit leaves. These results facilitate and deepen our understanding of how the light environment affects leaf structure and function and, therefore, provide the theoretical basis for understanding plant ecological strategies in response to the light environment.
Oil discovery, boom‐bust cycle and manufacturing slowdown: Evidence from a large industry level dataset
Authors: Alsharif Nouf , Bhattacharyya Sambit 
Published: October 2023

AbstractWe investigate the effects of giant oil discovery and boom‐bust price cycle on manufacturing using a large dataset of up to 49,481 two‐digit industry‐years across 136 countries over the period 1962 to 2012. We find that oil discovery reduces growth in manufacturing value added and wages. The effect on employment is insignificant. We also find strong association between oil discovery and manufacturing slowdown episodes. Oil price boom and bust both negatively affects manufacturing perhaps due to increasing input cost (boom) and declining demand (bust). We do not find any evidence in favour of a real exchange rate appreciation driven effect as outlined in standard Dutch Disease models. We speculate that the effect is primarily driven by an increase in the cost of locally sourced manufacturing input.
Local Search and the Evolution of World Models
Authors: Bramley Neil R. , Zhao Bonan , Quillien Tadeg , Lucas Christopher G. 
Published: October 2023

AbstractAn open question regarding how people develop their models of the world is how new candidates are generated for consideration out of infinitely many possibilities. We discuss the role that evolutionary mechanisms play in this process. Specifically, we argue that when it comes to developing a global world model, innovation is necessarily incremental, involving the generation and selection among random local mutations and recombinations of (parts of) one's current model. We argue that, by narrowing and guiding exploration, this feature of cognitive search is what allows human learners to discover better theories, without ever grappling directly with the problem of finding a “global optimum,” or best possible world model. We suggest this aspect of cognitive processing works analogously to how blind variation and selection mechanisms drive biological evolution. We propose algorithms developed for program synthesis provide candidate mechanisms for how human minds might achieve this. We discuss objections and implications of this perspective, finally suggesting that a better process‐level understanding of how humans incrementally explore compositional theory spaces can shed light on how we think, and provide explanatory traction on fundamental cognitive biases, including anchoring, probability matching, and confirmation bias.
Evolution of sea‐surfing plant propagule as revealed by the genomes of Heritiera mangroves
Authors: Wang Jiayan , Xie Wei , Si Fa , He Ziwen , Wang Xinfeng , Shao Shao , Shi Suhua , Guo Zixiao 
Published: October 2023

SUMMARYCoastal forests, such as mangroves, protect much of the tropical and subtropical coasts. Long‐distance dispersal via sea‐surfing propagules is essential for coastal plants, but the genomic and molecular basis of sea‐surfing plant propagule evolution remains unclear. Heritiera fomes and Heritiera littoralis are two coastal plants with typical buoyant fruits. We de novo sequenced and assembled their high‐quality genomes. Our phylogenomic analysis indicates H. littoralis and H. fomes originated (at ~6.08 Mya) just before the start of Quaternary sea‐level fluctuations. Whole‐genome duplication occurred earlier, permitting gene copy gains in the two species. Many of the expanded gene families are involved in lignin and flavonoid biosynthesis, likely contributing to buoyant fruit emergence. It is repeatedly revealed that one duplicated copy to be under positive selection while the other is not. By examining H. littoralis fruits at three different developmental stages, we found that gene expression levels remain stable from young to intermediate. However, ~1000 genes are up‐regulated and ~ 3000 genes are down‐regulated as moving to mature. Particularly in fruit epicarps, the upregulation of WRKY12 and E2Fc likely constrains the production of p‐Coumaroyl‐CoA, the key internal substrate for lignin biosynthesis. Hence, to increase fruit impermeability, methylated lignin biosynthesis is shut down by down‐regulating the genes CCoAOMT, F5H, COMT, and CSE, while unmethylated lignins are preferentially produced by upregulating CAD and CCR. Similarly, cutin polymers and cuticular waxes accumulate with high levels before maturation in epicarps. Overall, our genome assemblies and analyses uncovered the genomic evolution and temporal transcriptional regulation of sea‐surfing propagule.
Cuttings Transport With Oil- and Water-Based Drilling Fluids
Authors: Ytrehus Jan David , Lund Bjørnar , Taghipour Ali , Saasen Arild 
Published: October 2023

Abstract
Deviated well sections are common in most modern offshore well construction designs. In the North Sea region, which is a good example of mature areas, practically all producer or injector wells have highly deviated well sections. These wells must be constructed in an optimal manner with respect to functionality, drill time, risk, and all affiliated costs. Throughout the years, most hole-cleaning and hydraulic models have been developed based on experimental results from relatively small-scale laboratory tests with model fluids. Hole-cleaning properties and hydraulic behavior of practical drilling fluids intended for field application differ from those of most model fluids. Furthermore, results from small diameter tests may not always be relevant for or scalable to field applications because of the presence of a huge number of dimensional quantities like velocity, fluid properties, time, length, and other scale differences. Hence, studies using sufficient large-scale experimental facilities in controlled laboratory environments with the application of various field-designed drilling fluids are necessary to improve engineering models and operational practices. The current paper presents results from such laboratory tests where field-applied drilling fluids have been used. In comparison tests, the different drilling fluids have similar density and viscosity functions within the relevant field-applied shear rate range. This shear rate range is also assessed in the tests. One of the drilling fluids is oil-based, and the other one is an inhibitive water-based drilling fluid of the KCl/polymer type.
Integrated analysis of gut and oral microbiome in men who have sex with men with HIV Infection
Authors: Li Shuang , Su Bin , Wu Hao , He Qiushui , Zhang Tong 
Published: October 2023

ABSTRACT

Human immunodeficiency virus (HIV) infection leads to severe deficiency in host immunity by depletion of CD4
+
T-cells, resulting in an imbalance between the human microbiome and host immune response. Alterations in both gut and oral microbiomes have been observed in people living with HIV (PLWH). However, the impact of an altered gut and oral microbiome on HIV disease progression and the relationship between them in PLWH have not been explored. In this longitudinal study, we enrolled acute HIV-infected men who have sex with men (MSM) (
n
= 15), chronic HIV-infected MSM (
n
= 15), and HIV-uninfected MSM controls (
n
= 15). We collected anal and throat swab samples at recruitment (W0) from all participants and at 12 wk after antiretroviral therapy (ART) (W12) from the patients and performed 16S rRNA gene sequencing of genomic DNAs extracted from these swabs. In HIV-infected individuals with CD4 T-cell counts < 350 cells/µL, the increase in abundance of
Streptococcus
in the oral microbiome was inversely correlated with that of
Streptococcus
in the gut microbiome (
r
= −0.490,
P
= 0.039). In addition, the lower CD4
+
T-cell counts (<200 cells/µL) were associated with the higher abundance of
Escherichia–Shigella
and the lower abundance of
Methylobacterium–Methylorubrum
of the gut microbiome in HIV-infected individuals. We demonstrate the alteration of gut microbiome resulting from HIV infection and ART and the relationship between the gut and oral microbiome in PLWH and controls. These findings highlight the need for a better understanding of the interactions between the oral and gut microbiome and its potential role in HIV disease progression.

IMPORTANCE
Our longitudinal integrated study has shown the marked alterations in the gut and oral microbiome resulting from acute and chronic HIV infection and from antiretroviral therapy. Importantly, the relationship between oral and gut microbiomes in people living with acute and chronic HIV infection and “healthy” controls has also been explored. These findings might contribute to a better understanding of the interactions between the oral and gut microbiomes and its potential role in HIV disease progression.