bluuebunny/crossref_metadata_2025_split huggingface dataset:
Perceived predation risk affects the development of among-individual behavioral variation in a naturally clonal freshwater fish
Authors: Scherer U , Laskowski K , Kressler M , Ehlman S , Wolf M , Bierbach D 
Published: November 2023

ABSTRACTPredation risk is a key driver of natural selection, influencing various aspects of prey behavior. While many studies focus on how predation risk affects average behavior at population level, less attention has been given to its potential impact on behavioral variation within prey populations. Here, we investigate the effect of perceived predation risk on among-individual behavioral variation in naturally clonal Amazon mollies. Juveniles were raised in two groups: one exposed to a predator during feeding (visual cues only) and the other one serving as a control group. We observed activity and feeding behavior (time spent feeding, visits to feeding spot) over a four-week period. (I) Individuals in the predator-exposed group were on average less active but there was no difference in average feeding behavior between the two groups, suggesting individuals strategically respond to threats based on behavior-specific cost-benefit trade-offs. (II) Among-individual behavioral variation was affected by perceived predation risk: in the absence of the predator, individuals developed pronounced differences in the time spent feeding while no such development was observed in the predator-exposed group. This result has the potential of affecting a wide range of fitness-relevant intraspecific interactions if lower among-individual feeding variation translate into reduced sizes differences. The presence of the predator initially reduced among-individual variation in activity and visits to the feeding spot, but these differences did not persist over time. Our findings highlight the importance of considering both population-level and individual-level responses to predation risk for a more comprehensive understanding of its ecological and evolutionary consequences.
MolLM: A Unified Language Model for Integrating Biomedical Text with 2D and 3D Molecular Representations
Authors: Tang Xiangru , Tran Andrew , Tan Jeffrey , Gerstein Mark B. 
Published: November 2023

AbstractMotivationThe current paradigm of deep learning models for the joint representation of molecules and text primarily relies on 1D or 2D molecular formats, neglecting significant 3D structural information that offers valuable physical insight. This narrow focus inhibits the models’ versatility and adaptability across a wide range of modalities. Conversely, the limited research focusing on explicit 3D representation tends to overlook textual data within the biomedical domain.ResultsWe present a unified pre-trained language model, MolLM, that concurrently captures 2D and 3D molecular information alongside biomedical text. MolLM consists of a text Transformer encoder and a molecular Transformer encoder, designed to encode both 2D and 3D molecular structures. To support MolLM’s self-supervised pre-training, we constructed 160K molecule-text pairings. Employing contrastive learning as a supervisory signal for cross-modal information learning, MolLM demonstrates robust molecular representation capabilities across 4 downstream tasks, including cross-modality molecule and text matching, property prediction, captioning, and text-prompted molecular editing. Through ablation, we demonstrate that the inclusion of explicit 3D representations improves performance in these downstream tasks.Availability and implementationOur code, data, and pre-trained model weights are all available athttps://github.com/gersteinlab/MolLM.
Accountability and the metaverse: unaccounted digital worlds between techwashing mechanisms and new emerging meanings
Authors: Massaro Maurizio , Spanò Rosanna , Kuruppu Sanjaya Chinthana 
Published: November 2023

PurposeThis paper aims to understand the main challenges connected with accountability issues across multiple layers of the metaverse, to identify whether and how any techwashing is taking place and to discuss implications for accounting research.Design/methodology/approachTo develop the research, the authors refer to a critical dialogic accountability framework, operationalized in the current paper by leveraging the perspectives of accountability as virtues and as mechanisms (Bovens, 2010). The authors discuss who is accountable to whom, for what and in what manner in a relatively unregulated and unaccountable world, through the layers of virtual reality introduced by MacKenzieet al. (2013) and Llewellyn (2007). Methodologically, the study concentrates on 32 start-ups working in the metaverse selected from the Crunchbase database and relies on interviews, direct observation in the field and white paper reports analyzed by means of NVivo coding.FindingsThe findings show how metaverse creators deal with accountability as a virtue and accountability as a mechanism. Companies who operate metaverses primarily consider accountability in the virtual-physical domain, which focuses on developing the necessary internal and external architecture to enable a particular metaverse to function. Metaverse companies also emphasize the virtual-agential dimension that concentrates on onboarding, engaging with and incentivizing individuals in virtual worlds. There is an emphasis on outlining the virtues or standards that metaverse companies aspire to, but there is very little detail provided. Similarly, there are uneven and limited discussions of the mechanisms that can support accountability in most layers of a virtual world.Research limitations/implicationsThe analysis raises significant questions about the purpose, scope and use of metaverses, which are still a relatively unregulated and unaccountable world. The paper advances the idea that the current creators of metaverses are “techwashing” their projects, providing a utopian ideal of what their universes will look like but obfuscating the realities of their ventures in tech jargon that few people are likely to understand. Therefore, meaning and truth at all levels of the real and virtual worlds remain unaddressed, with implications to be explored in terms of legitimacy and trust of metaverses and the interests that shape them.Originality/valueThis paper is one of the first to address the issue of accountability in metaverses. It advances an analytical framework to guide future accounting and accountability research into virtual worlds.
Book review: Harsh Mander, Between Memory and Forgetting: Massacre and the Modi Years in Gujarat, Harsh Mander, Partitions of the Heart: Unmaking the Idea of India and Harsh Mander, Locking Down the Poor: The Pandemic and India’s Moral Centre
Authors: Habib Irfan 
Published: November 2023

Harsh Mander, Between Memory and Forgetting: Massacre and the Modi Years in Gujarat (New Delhi: Yoda Press), 2019, 292 pp., ₹450 (Pb). Harsh Mander, Partitions of the Heart: Unmaking the Idea of India (Gurgaon: Penguin-Viking), 2018, 290 pp., ₹599 (Hb). Harsh Mander, Locking Down the Poor: The Pandemic and India’s Moral Centre (New Delhi: Speaking Tiger Books), 2021, 231 pp., ₹399 (Pb).
Prognostic potential of whole exome sequencing in the clinical management of metachronous colorectal cancer liver metastases
Authors: Heczko Lucie , Hlaváč Viktor , Holý Petr , Dvořák Pavel , Liška Václav , Vyčítal Ondřej , Fiala Ondřej , Souček Pavel 
Published: November 2023

Abstract
Background
Colorectal cancer is a highly prevalent and deadly. The most common metastatic site is the liver. We performed a whole exome sequencing analysis of a series of metachronous colorectal cancer liver metastases (mCLM) and matched non-malignant liver tissues to investigate the genomic profile of mCLM and explore associations with the patients’ prognosis and therapeutic modalities.

Methods
DNA samples from mCLM and non-malignant liver tissue pairs (n = 41) were sequenced using whole exome target enrichment and their germline and somatic genetic variability, copy number variations, and mutational signatures were assessed for associations with relapse-free (RFS) and overall survival (OS).

Results
Our genetic analysis could stratify all patients into existing targeted therapeutic regimens. The most commonly mutated genes in mCLM were TP53, APC, and KRAS together with PIK3CA and several passenger genes like ABCA13, FAT4, PCLO, and UNC80. Patients with somatic alterations in genes from homologous recombination repair, Notch, and Hedgehog pathways had significantly prolonged RFS, while those with altered MYC pathway genes had poor RFS. Additionally, alterations in the JAK-STAT pathway were prognostic of longer OS. Patients bearing somatic variants in VIPR2 had significantly shorter OS and those with alterations in MUC16 prolonged OS. Carriage of the KRAS-12D variant was associated with shortened survival in our and external datasets. On the other hand, tumor mutation burden, mismatch repair deficiency, microsatellite instability, mutational signatures, or copy number variation in mCLM had no prognostic value.

Conclusions
The results encourage further molecular profiling for personalized treatment of colorectal cancer liver metastases discerning metachronous from synchronous scenarios.
The effects of ARID1A mutation in gastric cancer and its significance for treatment
Authors: Lu Shan , Duan Ruifeng , Cong Liang , Song Ying 
Published: November 2023

AbstractGastric cancer (GC) has emerged as a significant issue in public health all worldwide as a result of its high mortality rate and dismal prognosis. AT-rich interactive domain 1 A (ARID1A) is a vital component of the switch/sucrose-non-fermentable (SWI/SNF) chromatin remodeling complex, and ARID1A mutations occur in various tumors, leading to protein loss and decreased expression; it then affects the tumor biological behavior or prognosis. More significantly, ARID1A mutations will likely be biological markers for immune checkpoint blockade (ICB) treatment and selective targeted therapy. To provide theoretical support for future research on the stratification of individuals with gastric cancer with ARID1A as a biomarker to achieve precision therapy, we have focused on the clinical significance, predictive value, underlying mechanisms, and possible treatment strategies for ARID1A mutations in gastric cancer in this review.
Monetary shocks and production network in the G7 countries
Authors: Simionescu Mihaela , Schneider Nicolas 
Published: November 2023

AbstractUnderstanding the structure and properties of production networks is essential to identify the transmission channels from monetary shocks. While growingly studied, this literature keeps displaying critical caveats from which the investigation of G-7 economies is not spared. To fill this gap, this paper applies a version of Time-Varying Parameters Bayesian Vector-Autoregressions models (TVP-VAR) and investigates the responses of production networks (upstream and downstream dynamics) to endogeneous monetary shocks on key macro-level indicators (GDP, GDP deflator, exchange rate, short-term and long-term interest rates). Two distinct time-lengths are considered: a test (i.e., 2000–2014) and a treated period (i.e., 2007–2009,”the Great Recession”). Prior, key statistical conditions are checked using a stepwise stationary testing framework including the Kwiatkowski–Phillips–Schmidt–Shin (Kapetanios et al. in J Economet 112(2):359–379, 2003—KPSS) and panel Breitung (Nonstationary panels, panel cointegration, and dynamic panels. Emerald Group Publishing Limited, London, 2001) unit root tests; followed by the Pesaran (General diagnostic tests for cross section dependence in panels, 2004) Cross-sectional Dependence (CD) test; and the Im–Pesaran–Shin (Im et al. in J Economet 115(1):53–74, 2003—IPS) test for unit root in the presence of heterogenous slope coefficients. Panel Auto-Regressive Distributed Lag Mean Group estimates (PARDL-MG) offer interesting short- and long-run monetary shocks-production networks response functions, stratified by country and sector. Findings clearly indicate that upstreamness forces dominated downstremness dynamics during the period 2000–2014, whereas the financial sector ermeges as the clear transmission channel through which monetary shocks affected the productive economy during the Great Recession. In general, we conclude that the prioduction structure influences the transmission of monetary shocks in the G-7 economies. Adequate policy implications are supplied, along with a methodological note on the forecasting potential of TVP-VAR methodologies when dealing with series exhibiting structural breaks.
Curriculum Reconstruction: Alignment of Profile, Body of Knowledge, and Learning Outcomes of the Indonesian Islamic Education Study Program
Authors: Eva Latipah  , Hasan Noorhaidi 
Published: November 2023

Purpose – The misalignment between the profile with the body of knowledge (BoK) and the graduates’ learning outcomes (LO) of the PAI Study Program has caused the unclear educational objectives of the PAI study program, requiring the reconstruction of the PAI curriculum. This study aims to examine the reconstruction process of the PAI curriculum including the Profile, BoK, and LO of the PAI.
Design/methods/approach –The research was conducted qualitatively using survey, interview, and documentation methods packaged in seminars, guest lectures, workshops, and Focus Group Discussions. The subjects in this study were 83 PAI Study Program managers from Sumatra, Jakarta and Jabodetabek, DIY and Central Java, East Java, and the Eastern regions; the interviews were carried out with 15 study program managers. The obtained data was processed through the stages of reduction, display, and interpretation.
Findings – The results showed: 1) there are 6 profiles of Indonesian PAI after being reduced from 51 profiles, namely PAI teachers in schools/madrasahs, educational consultants, research assistants, administrators of educational institutions, Da’i/muballigh, and edupreneurs, 2) PAI’s Body of Knowledge consists of four scientific families: PAI science (what to teach), teaching science (how to teach), education and psychology (how to discipline), Research methodology, philosophy, language, technology, edupreneur (how to produce), 3) Graduate learning outcomes include in-depth mastery of PAI science, teaching, pedagogic, and PAI development, as well as how to teach PAI science effectively.
Research implications/limitations – This research has implications for the importance of preparing graduate profiles based on tracer studies, rather than based on ‘personal wishes’; and Learning outcomes must be adjusted to the standardized BoK of the Study Program.
Originality/value – the importance of profile mapping based on tracer studies, the significance of PAI’s body of knowledge in achieving PAI goals, and the importance of graduate learning outcomes for the expertise of PAI graduates.
Cave Levels in the Dachstein Massif (Eastern Alps)
Authors: Rummler Lina , Plan Lukas 
Published: November 2023

Abstract
This paper investigates the vertical distribution of horizontal and subhorizontal cave passages in the Dachstein Massif of Austria. Cave passages that are confined to vertical ranges, so-called cave levels, can be correlated with former valley floors and thus reflect tectonically and climatically stable periods. Previous studies analyzed significant karst Massifs (or parts of them) in the Northern Calcareous Alps but have excluded the Dachstein massif so far. The Dachstein is the second largest massif in the area, contains many extensive caves, and plays a key role in reconstruction of landscape evolution (“Dachstein surface”). In contrast to some previous works, we aimed to analyze only passages that formed (or are forming) under phreatic or epiphreatic conditions (i.e. permanently or episodically water-filled). This genetic classification is based on field observations, cave maps, 3D survey shots and descriptions. For this study, 789 caves with a total length of 279 km were considered, but data were only available for 599 caves (276 km). Only 25% of all caves in the Dachstein Massif are at least partly of (epi)phreatic origin, but the total length of phreatic passages is 204 km. Altitudes of the phreatic sections of each cave were grouped in 25-m increments and plotted according to their phreatic passage length. It turned out that there are five vertical accumulations of caves in the Dachstein Massif. Despite some previous studies that also considered morphological, hydrological, and sedimentological characteristics, our correlation with the “classical” supra-regional cave levels in other karst massifs was based only on elevation. The following elevations for the cave levels were determined: Spring Cave Level: 475-775 m a.s.l., Berger Cave Level: 825-1075 m, Giant Cave Level (with the highest peak): 1125-1550 m, Ruin Cave Level: 1600-2050 m, and a formerly unknown level at 2525-2750 m, for which we propose the name Voodoo Cave Level. According to this study the two longest cave systems, the Hirlatzhöhle (114 km long and 1560 m deep) and the Dachstein-Mammuthöhle (68 km, 1207 m) are most relevant for the result. The local vertical distribution of caves within the Dachstein was compared with the regional northward tilt of cave levels in the Northern Calcareous Alps, however the heterogeneous distribution of the known cave obscures local effects in the Dachstein Massif.
Biomineralization – A New Solution for Surface Casing Vent Flow
Authors: Griffin John , Bean Richard , Hiebert Randy 
Published: November 2023

Abstract
A new solution to the increasingly important issue of surface casing vent flow (SCVF), a biocementation process involving the squeezing of biomineralizing fluids was utilized on a Canadian well. Initially developed by the United States Department of Energy (DOE) for the purpose of sealing leaks in carbon sequestration wells, this technology has been utilized in over 100 oil and gas wells across the United States and Canada to seal and repair damaged cement, restore wellbore integrity, and prevent the unwanted flow of hydrocarbons up the production and surface casing annular. The following paper represents a case study detailing a risk-based approach and field deployment assessing the technology's effectiveness on a well in Alberta.
Abandonment operations which began on a well in Alberta, Canada in 2020 consisted of a series of zonal isolation plugs and cement retainer squeezes to eliminate surface casing vent flow. In March of 2023, with the vent flow still persistent at approximately 1 m3/day with 154 kPa build pressure, nonroutine abandonment operations began. The two previous cement retainer squeezes were drilled out down to the Mannville formation so new logs could be run. Biomineralization was identified as a viable solution to address SCVF on the well after initial analysis of the well indicated the presence of small aperture channels in the cemented annulus. In July 2023, the well was prepared for an annular squeeze utilizing biomineralization technology, and treatment commenced. Biomineralizing fluids were injected in intervals over the course of 48 hours, reducing injectivity by forming crystalline calcium carbonate, which has a similar chemical composition to limestone, to seal leakage pathways and eliminate gas flow.
Over the course of treatment, 219 L of biomineralizing fluids were pushed into leakage pathways, with the injection rate reduced from 0.776 lpm to 0.026 lpm, constituting a 97% reduction. The injection rates, pressures, and total volumes at the conclusion of treatment indicated successful sealing of micron-sized channels. Vent monitoring technology confirmed this via a steady reduction in flow over the course of treatment, and the total elimination of flow and bubbles at surface just seven days later. Biomineralization technology has been used as a solution for sealing and repairing micro annuli and other channels in annular cement by several operators to eliminate surface casing vent flow in Canada.
A polyphagous chewing herbivore induces positive plant-soil feedbacks of two legumes in soil with prolonged drought legacies
Authors: Hassan Kamrul , Maisnam Premchand , Carrillo Yolima , Nielsen Uffe 
Published: November 2023

Abstract

Plant-soil feedbacks (PSFs) occur when a plant species modifies soil physicochemical properties in ways that affect the growth of an individual subsequently grown in the same soil. PSFs are influenced by both herbivory, and climatic conditions, but it is unclear how foliar herbivory and climate change interact to modify PSFs. We conducted PSF experiment to assess the effect of foliar herbivory on Medicago sativa and Trifolium repens, when grown in monoculture and mixture. PSFs were assessed in soils from a field experiment simulating ambient rainfall and prolonged drought (50% reduction) for the past six years. All soils were sterilized and then re-inoculated to create the respective biological rainfall legacy treatments including sterile control. The cotton bollworm, Helicoverpa armigera, was used to induce herbivore treatments. Neither legume showed significant PSFs in the absence of herbivory. However, foliar herbivory induced positive PSFs for legumes in soil with drought legacies, and negative to neutral PSFs in soil with ambient rainfall legacies, when grown in monocultures. By contrast, herbivory induced strong positive PSFs in soils with ambient rainfall legacies, and negative PSFs in soils with drought legacies, in mixtures, possibly due to competition for space and resources. Herbivory-induced PSFs in soils with prolonged drought legacies appeared to be related to differences in leaf N (%) and rhizobia colonization likely due to effects on herbivore-induced systemic resistance. Our results indicate that foliar herbivores alter plant species co-existence and community dynamics under future climate change scenarios through changes in PSFs.
Effects of systolic blood pressure and antihypertensive medications on individuals with ST-elevation myocardial infarction
Authors: Chen Tao , Zhang Xueshan , Qian Wei , Zhou Ran , Su Mingyu , Ma Yanfeng 
Published: November 2023

Abstract
Background
To assess the associations of in-hospital antihypertensive medication use, admission systolic blood pressure (SBP), and 30-day outcome in individuals with ST-elevation myocardial infarction (STEMI).
Methods
STEMI cases treated in the Affiliated Hospital of Xuzhou Medical University between June 2010 and July 2021 were retrospectively analyzed. The primary outcome was 30-day all-cause mortality. Multivariate logistic regression analysis was performed to evaluate the associations of the number of used antihypertensive medications on 30-day mortality with admission SBP.
Results
Totally 7510 individuals with STEMI were included. After adjustment for baseline variables, SBP (OR = 1.12, 95%CI 1.08–1.19; P < 0.001), DBP (per 10-mmHg higher, OR = 1.14, 95%CI 1.04–1.22; P = 0.003), age (OR = 1.77, 95%CI 1.62–1.93; P < 0.001), male sex (OR = 1.56, 95%CI 1.31–1.86; P < 0.001), heart rate (OR = 1.19, 95%CI 1.11–1.22; P < 0.001), history of diabetes (OR = 1.50, 95%CI 1.18–1.91; P = 0.001), history of stroke (OR = 1.35, 95%CI 1.05–1.74; P = 0.002), Killip classes II-IV (ORs = 0.30–0.43, all P < 0.01), statin use (OR = 0.54, 95%CI 0.45–0.64; P < 0.001), nitrate use (OR = 0.70, 95%CI 0.53–0.92; P = 0.01), and use of a antihypertensive agent (OR = 9.91, 95%CI 3.86–25.48; P < 0.001) were independent predictors of 30-day mortality.
Conclusions
The number of antihypertensive medications during hospitalization has a significant association with 30-day mortality in Chinese individuals with STEMI without reperfusion.
Trial registration:
Not applicable.