bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the challenges of predicting treatment response in Hodgkin’s Lymphoma using transcriptomic data
Authors: Patrício André , Costa Rafael S. , Henriques Rui 
Published: July 2023

Abstract
Background
Despite the advancements in multiagent chemotherapy in the past years, up to 10% of Hodgkin’s Lymphoma (HL) cases are refractory to treatment and, after remission, patients experience an elevated risk of death from all causes. These complications are dependent on the treatment and therefore an increase in the prognostic accuracy of HL can help improve these outcomes and control treatment-related toxicity. Due to the low incidence of this cancer, there is a lack of works comprehensively assessing the predictability of treatment response, especially by resorting to machine learning (ML) advances and high-throughput technologies.

Methods
We present a methodology for predicting treatment response after two courses of Adriamycin, Bleomycin, Vinblastine and Dacarbazine (ABVD) chemotherapy, through the analysis of gene expression profiles using state-of-the-art ML algorithms. We work with expression levels of tumor samples of Classical Hodgkin’s Lymphoma patients, obtained through the NanoString’s nCounter platform. The presented approach combines dimensionality reduction procedures and hyperparameter optimization of various elected classifiers to retrieve reference predictability levels of refractory response to ABVD treatment using the regulatory profile of diagnostic tumor samples. In addition, we propose a data transformation procedure to map the original data space into a more discriminative one using biclustering, where features correspond to discriminative putative regulatory modules.

Results
Through an ensemble of feature selection procedures, we identify a set of 14 genes highly representative of the result of an fuorodeoxyglucose Positron Emission Tomography (FDG-PET) after two courses of ABVD chemotherapy. The proposed methodology further presents an increased performance against reference levels, with the proposed space transformation yielding improvements in the majority of the tested predictive models (e.g. Decision Trees show an improvement of 20pp in both precision and recall).

Conclusions
Taken together, the results reveal improvements for predicting treatment response in HL disease by resorting to sophisticated statistical and ML principles. This work further consolidates the current hypothesis on the structural difficulty of this prognostic task, showing that there is still a considerable gap to be bridged for these technologies to reach the necessary maturity for clinical practice.
The Emerging Therapeutic Potential of Kisspeptin and Neurokinin B
Authors: Patel Bijal , Koysombat Kanyada , Mills Edouard G , Tsoutsouki Jovanna , Comninos Alexander N , Abbara Ali , Dhillo Waljit S 
Published: July 2023

Abstract
Kisspeptin (KP) and neurokinin B (NKB) are neuropeptides that govern the reproductive endocrine axis through regulating hypothalamic gonadotropin-releasing hormone (GnRH) neuronal activity and pulsatile GnRH secretion. Their critical role in reproductive health was first identified after inactivating variants in genes encoding for KP or NKB signaling were shown to result in congenital hypogonadotropic hypogonadism and a failure of pubertal development. Over the past 2 decades since their discovery, a wealth of evidence from both basic and translational research has laid the foundation for potential therapeutic applications. Beyond KP's function in the hypothalamus, it is also expressed in the placenta, liver, pancreas, adipose tissue, bone, and limbic regions, giving rise to several avenues of research for use in the diagnosis and treatment of pregnancy, metabolic, liver, bone, and behavioral disorders.
The role played by NKB in stimulating the hypothalamic thermoregulatory center to mediate menopausal hot flashes has led to the development of medications that antagonize its action as a novel nonsteroidal therapeutic agent for this indication. Furthermore, the ability of NKB antagonism to partially suppress (but not abolish) the reproductive endocrine axis has supported its potential use for the treatment of various reproductive disorders including polycystic ovary syndrome, uterine fibroids, and endometriosis. This review will provide a comprehensive up-to-date overview of the preclinical and clinical data that have paved the way for the development of diagnostic and therapeutic applications of KP and NKB.
Contraceptive Behavior Dynamics and Unintended Pregnancy: A Latent Transition Analysis
Authors: Swiatlo Alison , Curtis Sian , Gottfredson Nisha , Halpern Carolyn , Tumlinson Katherine , Lich Kristen Hassmiller 
Published: July 2023

Abstract
The average U.S. woman wants to have two children; to do so, she will spend about three years pregnant, postpartum, or trying to become pregnant, and three decades trying to avoid pregnancy. However, few studies have examined individual patterns of contraceptive use over time. These trajectories are important to understand given the high rate of unintended pregnancy and how little we know about the complex relationship between contraceptive use, pregnancy intention, and patterns of reproductive behavior. We use data from the 2015–2017 National Survey of Family Growth to examine reproductive behavior and pregnancies across three years of calendar data. We identify seven behavior typologies, their prevalence, how women transition between them, and how pregnancies affect transitions. At any given time, half of women are reliably using contraception. A small proportion belong to a high pregnancy risk profile of transient contraceptive users, but some transition to using condoms or other methods consistently. An unintended pregnancy may initiate a transition into stable contraceptive use for some women, although that is primarily condom use. These findings have important implications for the ways contraception fits into women's lives and how that behavior interacts with relationships, sex, and life stage trajectories.
An evaluation of a biophysical model for predicting avian thermoregulation in the heat
Authors: Conradie Shannon R. , Kearney Michael R. , Wolf Blair O. , Cunningham Susan J. , Freeman Marc T. , Kemp Ryno , McKechnie Andrew E. 
Published: July 2023

ABSTRACT
Survival and reproduction of endotherms depend on their ability to balance energy and water exchange with their environment, avoiding lethal deficits and maximising gains for growth and reproduction. At high environmental temperatures, diurnal endotherms maintain body temperature (Tb) below lethal limits via physiological and behavioural adjustments. Accurate models of these processes are crucial for predicting effects of climate variability on avifauna. We evaluated the performance of a biophysical model (NicheMapR) for predicting evaporative water loss (EWL), resting metabolic rate (RMR) and Tb at environmental temperatures approaching or exceeding normothermic Tb for three arid-zone birds: southern yellow-billed hornbill (Tockus leucomelas), southern pied babbler (Turdoides bicolor) and southern fiscal (Lanius collaris). We simulated metabolic chamber conditions and compared model outputs with thermal physiology data collected at air temperatures (Tair) between 10 and 50°C. Additionally, we determined the minimum data needed to accurately model diurnal birds' thermoregulatory responses to Tair using sensitivity analyses. Predicted EWL, metabolic rate and Tb corresponded tightly with observed values across Tair, with only minor discrepancies for EWL in two species at Tair≈35°C. Importantly, the model captured responses at Tair=30–40°C, a range spanning threshold values for sublethal fitness costs associated with sustained hot weather in arid-zone birds. Our findings confirm how taxon-specific parameters together with biologically relevant morphological data can accurately model avian thermoregulatory responses to heat. Biophysical models can be used as a non-invasive way to predict species’ sensitivity to climate, accounting for organismal (e.g. physiology) and environmental factors (e.g. microclimates).
Social experience influences thermal sensitivity: lessons from an amphibious mangrove fish
Authors: Melanson Chloé A. , Lamarre Simon G. , Currie Suzanne 
Published: July 2023

ABSTRACT
Understanding the factors affecting the capacity of ectothermic fishes to cope with warming temperature is critical given predicted climate change scenarios. We know that a fish's social environment introduces plasticity in how it responds to high temperature. However, the magnitude of this plasticity and the mechanisms underlying socially modulated thermal responses are unknown. Using the amphibious hermaphroditic mangrove rivulus fish Kryptolebias marmoratus as a model, we tested three hypotheses: (1) social stimulation affects physiological and behavioural thermal responses of isogenic lineages of fish; (2) social experience and acute social stimulation result in distinct physiological and behavioural responses; and (3) a desensitization of thermal receptors is responsible for socially modulated thermal responses. To test the first two hypotheses, we measured the temperature at which fish emerged from the water (i.e. pejus temperature) upon acute warming with socially naive isolated fish and with fish that were raised alone and then given a short social experience prior to exposure to increasing temperature (i.e. socially experienced fish). Our results did not support our first hypothesis as fish socially stimulated by mirrors during warming (i.e. acute social stimulation) emerged at similar temperatures to isolated fish. However, in support of our second hypothesis, a short period of prior social experience resulted in fish emerging at a higher temperature than socially naive fish suggesting an increase in pejus temperature with social experience. To test our third hypothesis, we exposed fish that had been allowed a brief social interaction and naive fish to capsaicin, an agonist of TRPV1 thermal receptors. Socially experienced fish emerged at significantly higher capsaicin concentrations than socially naive fish suggesting a desensitization of their TRPV1 thermal receptors. Collectively, our data indicate that past and present social experiences impact the behavioural response of fish to high temperature. We also provide novel data suggesting that brief periods of social experience affect the capacity of fish to perceive warm temperature.
Facile Preparation of Near Infrared-Luminescent Protein Complexes with Conjugated Polymers Consisting of Boron Azobenzene Units
Authors: Yoo Dahye , Nakamura Masashi , Kanjo Misato , Gon Masayuki , Watanabe Hiroyuki , Kita Hiroshi , Tanaka Kazuo 
Published: July 2023

Abstract
We report herein facile preparation of near infrared (NIR)-luminescent protein complexes with conjugated polymers. We have discovered that solid-state luminescence in the NIR region can be obtained from the series of conjugated polymers consisting of boron azobenzene complexes. We demonstrate in this paper that protein molecules can be modified through adsorption with the boron azobenzene-containing conjugated polymers simply by mixing in an aqueous buffer and subsequently purification with filtration followed by freeze drying. The modified protein complexes can exhibit NIR emission in the buffer and high dispersibility. In particular, comparing to the complex with indocyanine green (ICG), which is a conventional NIR-luminescent dye, polymer-modified protein complexes showed higher resistance to photobleaching. Finally, by using lipase as a scaffold, we confirmed that enzymatic activity can be detected after polymer modification.
Stigma and discrimination against transgender men in Bhutan
Authors: Saxena Vinita , Xu Audrey , Kinley Kinley , Tsheten Tashi , Gyeltshen Tenzin , Tobgay Tashi , Zajkowski Tae Young , McFarland Willi , Khandu Lekey 
Published: July 2023

BackgroundWhile transgender people worldwide face high rates of stigma and discrimination, there are few studies of transgender men (also “trans men”) in Asia. We measured the prevalence of, and factors associated with, stigma and discrimination faced by trans men in Bhutan to bring visibility to their experiences and inform health and social policy changes.MethodsThis cross-sectional survey was conducted in nine regions in Bhutan from November 2019 to January 2020. A total of 124 trans men were recruited using a hybrid venue-based and peer-referral approach. Data were collected using an interviewer-administered questionnaire. Multivariate logistic regression characterized associations with experiencing stigma and discrimination when accessing health services.FindingsParticipants were young (48.0% 18–24 years) and 48.4% had migrated from a rural to an urban area. The majority (95.2%) experienced stigma because people knew or thought they were trans men. Associations with frequent experiences of stigma were living with their partner as a couple (adjusted odds ratio [AOR] 3.07, 95% CI 1.27–7.44) and being unemployed or a student (3.22, 1.44–7.19). Nearly half (47.6%) said they experienced discrimination when accessing health care because people knew or thought they were a trans man; this experience was associated with migration (2.42, 1.08–5.39) and having >15 trans men in their social network (3.73, 1.69–8.26). Most (94.4%) experienced verbal violence, 10.5% experienced physical violence, and 4.8% experienced sexual violence.InterpretationOur study found high rates of stigma, discrimination, and interpersonal violence due to being a trans man in Bhutan. Findings highlight the urgent need for strengthening laws and regulations to protect the rights of transgender persons, particularly when accessing health services, recognizing partnerships, and preventing violence in public spaces.
Association of chronic neutrophil activation with risk of mortality
Authors: Penn Marc S. , MacRae Calum , Goldfaden Rebecca F. , Choksi Rushab R. , Smith Steven , Wrenn David , Saghir Mouris X. , Klemes Andrea B. 
Published: July 2023

Background
Levels of free myeloperoxidase (MPO), a cardiovascular risk marker, have been reported to decline with standard care. Whether such declines signify decreased risk of mortality remains unknown.

Design
Cox proportional hazard models were generated using data from a retrospective cohort study of prospectively collected measures.

Participants
Patients (3,658) who had MPO measurements and LDL-C ≥ 90 mg/dL during 2011–2015 were selected based on a stratified random sampling on MPO risk level. Baseline MPO was either low (<470 pmol/L), moderate (470–539 pmol/L), or high (≥540 pmol/L).

Main outcomes and measures
First occurrence of MACE (myocardial infarction, stroke, coronary revascularization, or all-cause death).

Results
Mean age was 66.5 years, and 64.7% were women. During a mean 6.5-year follow-up, crude incidence per 1000 patient years was driven by death. The incidence and all-cause death was highest for patients with high MPO (21.2; 95% CI, 19.0–23.7), then moderate (14.6; 95% CI, 11.5–18.5) and low (2.3; 95% CI, 1.2–4.6) MPO. After adjusting for age, sex, and cardiovascular risk factors, risk of cardiovascular death did not differ significantly between patients with high and low MPO (HR, 1.57; 95% CI, 0.56–4.39), but patients with high MPO had greater risk of non-cardiovascular (HR, 6.15; 95% CI, 2.27–16.64) and all-cause (HR, 3.83; 95% CI, 1.88–7.78) death. During follow-up, a 100 pmol/L decrease in MPO correlated with a 5% reduction in mortality (HR, 0.95; 95% CI, 0.93–0.97) over 5 years.

Conclusions
Free circulating MPO is a strong marker of risk of mortality. Monitoring changes in MPO levels over time may provide insight into changes in physiology that mark a patient for increased risk of mortality.
A tale of two tool(kit)s: from canonical antonymy to non-canonical opposition in the Qur’anic discourse
Authors: Hassanein Hamada 
Published: July 2023

AbstractA number of discourse functions of canonical antonyms have been quantified and classified in English and across languages, each of which is associated with typical syntactic frames. Taking such a classification of canonical antonymy as an analytical toolkit, (Davies, Matt. 2012. A new approach to oppositions in discourse: the role of syntactic frames in the triggering of noncanonical oppositions.Journal of English Linguistics40(1). 41–73) quantified and qualified the role of these frames in triggering non-canonical oppositions in English news discourse. Synergizing the provisional typologies of canonical antonymy (Hassanein, Hamada. 2018. Discourse functions of opposition in Classical Arabic: The case in ḥadīth genre.Lingua201. 18–44; Jones, Steven. 2002.Antonymy: A corpus-based perspective. London and New York: Routledge.) and non-canonical opposition (Davies, Matt. 2012. A new approach to oppositions in discourse: the role of syntactic frames in the triggering of noncanonical oppositions.Journal of English Linguistics40(1). 41–73), this study has sought to develop a dynamic toolkit for the quantitative and qualitative analyses of non-canonical opposition across Arabic varieties and potentially other languages. The toolkit was tested quantitatively and qualitatively against a dataset of 2125 non-canonical oppositional pairs collected from the Qur’an with reference to the Qur’anic Arabic Corpus. Results showed that the syntactic frames which house a wide range of co-occurring canonical antonyms also house a wider range of non-canonical oppositions in binary and trinary representations of abstract and concrete entities. The role of syntactic frames in the triggering of non-canonical oppositions is quantitatively and qualitatively significant for locating and explicating the ideological repercussions of oppositions towards Qur’an interpretation. It is concluded that a synergy of typologies results in a replicable pathway for analysis.
Chemical Blast Standard (1 kg)
Authors: Kei Takazawa Samuel , Kim Keehoon , Garcés Milton 
Published: July 2023

Abstract
Chemical explosions create blast waves with large overpressure disturbances. It is important to develop a standard blast model based on data to accurately predict acoustic blast-wave amplitudes near detonations and invert for explosion energy from distant observations of blast-wave signals. However, open data from large, controlled chemical explosions with reliable ground truth can be challenging to find. The lack of access to such data could limit the number of contributions to related research and potentially stifle the rate of discoveries or validation of existing models. To address these data scarcity problem, we have curated and compiled a standardized set of 817 blast-wave waveforms from 19 distinct high-explosive events. The blast-wave waveforms are standardized to a 1 kg trinitrotoluene explosion using scaling laws and corrections for location effects. A brief overview of the dataset is presented along with explosion feature models as well as recommendations for extracting explosion features. The resulting dataset is distributed to an open repository in both Seismic Analysis Code and pandas DataFrame formats containing the waveforms, the scaled distances, and the sample rates.
Increased Risk of Venous Thromboembolism in Patients with Postoperative Anemia After Total Joint Arthroplasty
Authors: Liu Kevin C. , Piple Amit S. , Richardson Mary K. , Mayer Lucas W. , Mayfield Cory K. , Christ Alexander B. , Lieberman Jay R. , Heckmann Nathanael D. 
Published: July 2023

Background:
The relationship between anemia and the risk of venous thromboembolism (VTE) following total knee arthroplasty (TKA) and total hip arthroplasty (THA) remains unclear. Red blood cell (RBC) transfusions, which have been shown to have thrombogenic effects, may explain conflicting data. This study sought to elucidate the relationship between anemia, RBC transfusions, and VTE following total joint arthroplasty (TJA).

Methods:
Using the International Classification of Diseases, Tenth Revision (ICD-10) and Current Procedural Terminology (CPT) codes, the Premier Healthcare Database was queried for all adults who underwent primary elective THA or TKA from January 2015 to December 2020. Patients were classified into 3 cohorts: those who did not have a diagnosis of anemia and did not receive an RBC transfusion (the control group), those with acute blood loss anemia who did not receive a transfusion (the anemia without transfusion group), and those with acute blood loss anemia who did receive a transfusion (the anemia with transfusion group). The primary outcomes assessed were the 90-day rate and risk of deep vein thrombosis (DVT), pulmonary embolism (PE), and aggregate VTE. Analysis of variance and pairwise comparisons were used to compare groups. Multivariable analyses were performed to account for confounding factors.

Results:
The 1,290,815 patients identified as having undergone TJA included 1,078,507 control patients (83.6%), 198,233 patients who had anemia without transfusion (15.4%), and 14,075 patients who had anemia and transfusion (1.1%). Age, sex, race, length of hospital stay, and hospital costs were significantly different between the 3 groups. After adjusting for confounding factors, there was no difference between the anemia without transfusion group and the control group with regard to DVT (adjusted odds ratio [OR], 0.97 [95% confidence interval (CI), 0.89 to 1.06]; p = 0.500), PE (adjusted OR, 1.04 [95% CI, 0.92 to 1.18]; p = 0.543), and VTE (adjusted OR, 0.99 [95% CI, 0.92 to 1.06]; p = 0.697). However, patients with anemia and transfusion had an increased risk of PE (adjusted OR, 1.83 [95% CI, 1.34 to 2.51]; p < 0.001) and VTE (adjusted OR, 1.39 [95% CI, 1.14 to 1.70]; p = 0.001) compared with patients in the control group.

Conclusions:
Patients with acute blood loss anemia who received a transfusion were at increased risk for developing VTE following TJA, whereas patients with anemia who did not receive a transfusion were not. Orthopaedic surgeons need to be aware of the risks of transfusion and individualize the use of transfusions in their patients.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.