bluuebunny/crossref_metadata_2025_split huggingface dataset:
Answering Topical Information Needs Using Neural Entity-Oriented Information Retrieval and Extraction
Authors: Chatterjee Shubham 
Published: January 2023

In the modern world, search engines are an integral part of human lives. The field of Information Retrieval (IR) is concerned with finding material (usually documents) of an unstructured nature (usually text) that satisfies an information need (query) from within large collections (usually stored on computers). The search engine then displays a ranked list of results relevant to our query. Traditional document retrieval algorithms match a query to a document using the overlap of words in both. However, the last decade has seen the focus shifting to leveraging the rich semantic information available in the form of
entities.

Entities are uniquely identifiable objects or things such as places, events, diseases, etc. that exist in the real or fictional world. Entity-oriented search systems leverage the semantic information associated with entities (e.g., names, types, etc.) to better match documents to queries. Web search engines would provide better search results if they understand the meaning of a query.
This dissertation advances the state-of-the-art in IR by developing novel algorithms that understand text (query, document, question, sentence, etc.) at the semantic level. To this end, this dissertation aims to understand the fine-grained meaning of entities from the context in which the entities have been mentioned, for example, "oysters" in the context of food versus ecosystems. Further, this dissertation aims to automatically learn (vector) representations of entities that incorporate this fine-grained knowledge and knowledge about the query. This dissertation refines the automatic understanding of text passages using deep learning, a modern artificial intelligence paradigm.
This dissertation utilizes the semantic information extracted from entities to retrieve materials (text and entities) relevant to a query. The interplay between text and entities in the text is studied by addressing three related prediction problems: (1) Identify entities that are relevant for the query, (2) Understand an entity's meaning in the context of the query, and (3) Identify text passages that elaborate the connection between the query and an entity.

The research presented in this dissertation may be integrated into a larger system designed for answering complex topical queries such as
dark chocolate health benefits
which require the search engine to automatically understand the connections between the query and the relevant material, thus transforming the search engine into an answering engine.

Awarded by:
University of New Hampshire, Durham, USA on 1 September 2022.

Supervised by:
Laura Dietz.

Available at:
https://scholars.unh.edu/dissertation/2714/.
Choice of Survival Metric and Its Impacts on Cancer Survival Estimates for American Indian and Alaska Native People
Authors: Nash Sarah H. , Wahlen Madison M. , Meisner Angela L W. , Morawski Bożena M. 
Published: February 2023

AbstractBackground:Different survival metrics have different applicability to clinical practice and research. We evaluated how choice of survival metric influences assessment of cancer survival among American Indian and Alaska Native (AIAN) people relative to non-Hispanic Whites (NHW). A secondary objective was to present variations in survival among AIAN people by age, sex, stage, and Indian Health Service (IHS) region.Methods:Five-year survival was calculated using the North American Association of Central Cancer Registries Cancer in North America dataset. We calculated survival among AIAN people, compared with NHW using four approaches: (i) observed (crude) survival, (ii) cause-specific survival, (iii) relative survival using age- and sex-adjusted lifetables, and (iv) relative survival using lifetables additionally adjusted for race, geography, and socioeconomic status. For AIAN people, we evaluated how survival varied by age, stage at diagnosis, and IHS region.Results:Observed survival methods produced the lowest estimates, and—excepting prostate cancer—cause-specific methods produced the highest survival estimates. Survival was lower among AIAN people than NHW for all methods. Among AIAN people, survival was higher among those 20–64 years, females, and tumors diagnosed at local stage. Survival varied by IHS region and cancer sites.Conclusions:These results support the assertion that using the same methodology to compare survival estimates between racial and ethnic groups is of paramount importance, but that the choice of metric requires careful consideration of study objectives.Impact:These findings have the potential to impact choice of survival metric to explore disparities among AIAN people.
Payload-Binding Fab Fragments Increase the Therapeutic Index of MMAE Antibody–Drug Conjugates
Authors: Bordeau Brandon M. , Nguyen Toan Duc , Polli Joseph Ryan , Chen Ping , Balthasar Joseph P. 
Published: February 2023

AbstractMonomethyl auristatin E (MMAE) is a potent tubulin inhibitor that is used as the payload for four FDA-approved antibody–drug conjugates (ADC). Deconjugated MMAE readily diffuses into untargeted cells, resulting in off-target toxicity. Here, we report the development and evaluation of a humanized Fab fragment (ABC3315) that enhances the therapeutic selectivity of MMAE ADCs. ABC3315 increased the IC50 of MMAE against human cancer cell lines by &gt; 500-fold with no impact on the cytotoxicity of MMAE ADCs, including polatuzumab vedotin (PV) and trastuzumab-vc-MMAE (TvcMMAE). Coadministration of ABC3315 did not reduce the efficacy of PV or TvcMMAE in xenograft tumor models. Coadministration of ABC3315 with 80 mg/kg TvcMMAE significantly (P &lt; 0.0001) increased the cumulative amount of MMAE that was excreted in urine 0 to 4 days after administration from 789.4±19.0 nanograms (TvcMMAE alone) to 2625±206.8 nanograms (for mice receiving TvcMMAE with coadministration of ABC3315). Mice receiving 80 mg/kg TvcMMAE and PBS exhibited a significant drop in white blood cell counts (P = 0.025) and red blood cell counts (P = 0.0083) in comparison with control mice. No significant differences, relative to control mice, were found for white blood cell counts (P = 0.15) or for red blood cell counts (P = 0.23) for mice treated with 80 mg/kg TvcMMAE and ABC3315. Coadministration of ABC3315 with 120 mg/kg PV significantly (P = 0.045) decreased the percentage body weight loss at nadir for treated mice from 11.9%±7.0% to 4.1%±2.1%. Our results demonstrate that ABC3315, an anti-MMAE Fab fragment, decreases off-target toxicity while not decreasing antitumor efficacy, increasing the therapeutic window of MMAE ADCs.
Perspectives on Malay Language Use and Autonym Preference Among Urban Malays in South Thailand
Authors: Joll Christopher M. , Aree Srawut 
Published: January 2023

Abstract
This article offers theoretical and ethnographic perspectives on language ideology and autonym preference among bi-lingual urban Malays in Pattani’s provincial capital. The first of its two substantive sections presents a concise summary of the most relevant insights provided by linguistic anthropologists and sociolinguists who have written on language ideology and the role of language in identity formation. The primary purpose of the second section is to explore the heuristic utility of these theoretical insights on a range of ethnographic vignettes where a range of language-related issues have historically represented a significant source of mistrust between the local Malay majority and Bangkok. We develop insights provided by interactionalist perspectives on language and identity formation to Malay identity formation, specifically which autonyms are strategically adopted.
Citrobacter keratitis: predisposing factors and clinical characteristics
Authors: Soleimani Mohammad , Masoumi Ahmad , Tabatabaei Seyed Ali , Zamani Mohammad Hossein 
Published: January 2023

Abstract
Purpose
To report predisposing factors, clinical presentation, antibiotic sensitivity, and management of Citrobacter-caused infectious keratitis.

Methods
We retrospectively reviewed the medical records of culture-proven cases of Citrobacter keratitis in a tertiary referral center for 8 years (from January 2012 to September 2020). Demographic data of the patients, predisposing factors, and presenting signs were extracted.

Results
Eighteen cases of microbial keratitis due to Citrobacter spp. were identified. The median age of the patients was 66 years (range: 10–89, interquartile range : 59–81). Thirteen patients were male and 5 were female. Multiple predisposing factors were identified in all eyes, including ocular surface disease (n = 8), previous corneal surgery (n = 6), and history of ocular trauma (n = 6). Five patients were diabetic. Corrected distance visual acuity (CDVA) of patients was light perception (LP) in 8 patients, hand motion (HM) in 7, counting fingers (CF) at 1 m in 1, and CF at 2 m in 2 patients. Thirteen eyes exhibited hypopyon. An area of corneal thinning was observed in 7 eyes (38.9%). Endophthalmitis due to infectious keratitis developed in one patient. In vitro susceptibility testing confirmed high sensitivity to ceftazidime and aminoglycosides. Medical management consisted primarily of topical amikacin (20 mg/ml) combined with topical cefazoline (50 mg/ml) (72.2%). Surgical tectonic procedures were carried out in 7 eyes (38.9%).

Conclusion
Citrobacter spp. is a rare cause of bacterial keratitis.Previous keratoplasty and ocular surface problems are important risk factors. The prognosis is not good and surgical tectonic intervention is required in many cases to resolve the corneal infection.
In it for the long run: perspectives on exploiting long-read sequencing in livestock for population scale studies of structural variants
Authors: Nguyen Tuan V. , Vander Jagt Christy J. , Wang Jianghui , Daetwyler Hans D. , Xiang Ruidong , Goddard Michael E. , Nguyen Loan T. , Ross Elizabeth M. , Hayes Ben J. , Chamberlain Amanda J. , MacLeod Iona M. 
Published: January 2023

AbstractStudies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in the genome. However, unlike small variants (< 50 bp), it has been challenging to accurately identify and genotype SV at the population scale using short-read sequencing. Long-read sequencing technologies are becoming competitively priced and can address several of the disadvantages of short-read sequencing for the discovery and genotyping of SV. In livestock species, analysis of SV at the population scale still faces challenges due to the lack of resources, high costs, technological barriers, and computational limitations. In this review, we summarize recent progress in the characterization of SV in the major livestock species, the obstacles that still need to be overcome, as well as the future directions in this growing field. It seems timely that research communities pool resources to build global population-scale long-read sequencing consortiums for the major livestock species for which the application of genomic tools has become cost-effective.
Whole exome sequencing with a focus on cardiac disease-associated genes in families of sudden unexplained deaths in Yunnan, southwest of China
Authors: Wei Si-Jie , Du Jin-Liang , Wang Yue-Bing , Qu Peng-Fei , Ma Lin , Sun Zhong-Chun , Tang Xue , Liu Kai , Xi Yan-Mei , Nie Sheng-Jie , Jia Peng-Lin , Long Wu , Qu Yong-Qiang , Li Yu-Hua , Lei Pu-Ping 
Published: January 2023

Abstract
Objectives
To explore the causes of sudden unexpected death (SUD) and to search for high-risk people, whole exome sequencing (WES) was performed in families with SUDs.

Methods
Whole exome sequencing of 25 people from 14 SUD families were screened based on cardiac disease-associated gene variants, and their echocardiograms and electrocardiograms (ECG) were also examined. The protein function of mutated genes was predicted by SIFT, PolyPhen2 and Mutation Assessor.

Results
In the group of 25 people from 14 SUD families, 49 single nucleotide variants (SNVs) of cardiac disease-associated genes were found and verified by Sanger sequencing. 29 SNVs of 14 cardiac disorder-related genes were predicted as pathogens by software. Among them, 7 SNVs carried by two or more members were found in 5 families, including SCN5A (c.3577C > T), IRX4 (c.230A > G), LDB3 (c.2104 T > G), MYH6 (c.3G > A), MYH6 (c.3928 T > C), TTN (c.80987C > T) and TTN (c.8069C > T). 25 ECGs were collected. In summary, 4 people had J-point elevation, 2 people had long QT syndrome (LQTS), 4 people had prolonged QT interval, 3 people had T-wave changes, 3 people had sinus tachycardia, 4 people had sinus bradycardia, 4 people had left side of QRS electrical axis, and 3 people had P wave broadening. Echocardiographic results showed that 1 person had atrial septal defect, 1 person had tricuspid regurgitation, and 2 people had left ventricular diastolic dysfunction.

Conclusions
Of the 14 heart disease-associated genes in 14 SUDs families, there are 7 possible pathological SNVS may be associated with SUDs. Our results indicate that people with ECG abnormalities, such as prolonged QT interval, ST segment changes, T-wave change and carrying the above 7 SNVs, should be the focus of prevention of sudden death.
Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives
Authors: Li Xiaofeng , Wang Xingyu , Ma Qiangqiang , Zhong Yunfeng , Zhang Yibo , Zhang Ping , Li Yingzheng , He Ruyu , Zhou Yang , Li Yang , Cheng Mingjun , Yan Xu , Li Yan , He Jianmei , Iqbal Muhammad Zafar , Rong Tingzhao , Tang Qilin 
Published: January 2023

Abstract
Background
Tripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear.

Results
Single-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including “Flavonoid biosynthesis,” “Oxidoreductase activity,” and “Plant hormone signal transduction” in the leaves and roots, and “Iron ion binding,” “Acetyl-CoA carboxylase activity,” and “Serine-type carboxypeptidase activity” in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in “Spliceosome” and “MAPK signal pathway” dynamically responded to salt stress as salinity changed. Protein–protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance.

Conclusions
Our results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.
Integrated metabolome and transcriptome analysis unveils novel pathway involved in the fruit coloration of Nitraria tangutorum Bobr.
Authors: Zhang Huilong , Hu Aishuang , Wu Haiwen , Zhu Jianfeng , Zhang Jingbo , Cheng Tielong , Shabala Sergey , Zhang Huaxin , Yang Xiuyan 
Published: February 2023

Abstract
Background
The desert shrub Nitraria tangutorum Bobr. is important for its resistance to salt and alkali in Northwest China. It is an ecologically important species in this region and provides edible and medicinal berries. This study showed a mutant of N. tangutorum (named Jincan, JC) that has a strong yellow pericarp vs red in a wild type (represented by NT).

Results
In this study, the secondary metabolic and molecular mechanisms responsible for Nitraria fruit coloration were investigated using LC–MS-based widely targeted metabolomics and transcriptomics data. As a result of our study, 122 and 104 flavonoid metabolites were differentially expressed throughout the mature and transition stages between JC and NT, respectively. Furthermore, two cyanidin derivatives (cyanidin 3-O-glucoside and cyanidin-3-O-(2''-O-glucosyl) glucoside) and one pelargonidin derivative (pelargonidin-3-O-glucoside) were identified only in the NT phenotype. The functional genes F3H (flavanone 3-hydroxylase), F3'H (flavonoid 3′-hydroxylase) and UFGT (flavonoid 3-O-glucosyltransferase) and the transcription factors MYB, bHLH, NAC and bZIP were significantly downregulated in JC. Meanwhile, the activity of UFGT was extremely low in both periods of JC, with a five-fold higher enzymatic activity of UFGT in RT than in YT. In summary, due to the lack of catalysis of UGFT, yellow fruit of JC could not accumulate sufficient cyanidin and pelargonidin derivatives during fruit ripening.

Conclusion
Taken together, our data provide insights into the mechanism for the regulation of anthocyanin synthesis and N. tangutorum fruit coloration and provide a theoretical basis to develop new strategies for developing bioactive compounds from N. tangutorum fruits.
Prevalence and factors associated with post-traumatic stress disorder among internally displaced people in camps at Debre Berhan, Amhara Region, Ethiopia: a cross-sectional study
Authors: Makango Belay , Alemu Zewdie Aderaw , Solomon Tesfaye , Lemma Nigussie , Girma Tewodros , Mohammednur Tijani , Alayu Mikias , Fufa Yaregal 
Published: January 2023

Abstract
Background
Post-traumatic stress disorder (PTSD) is a common mental disorder after traumatic exposure that can have long-lasting physical and mental health consequences. In 2021, Ethiopia saw the highest number of internally displaced people (IDP) due to conflict and war with the scope of the internal displacement being very high in the study area and less attention has been given to mental health.

Objective
To determine the prevalence and associated factors of PTSD among internally displaced people in camps at Debre Berhan, Ethiopia.

Methods
A cross-sectional study was conducted from December 1–30, 2021 among 406 IDPs, who were selected by random systematic sampling from the registration and proportionally allocated to three IDP camps in Debre Berhan. Post-traumatic stress disorder was measured by the PTSD checklist (DSM-5). Data were collected through an interviewer-administered pre-tested questionnaire, entered into EpiData version 3.1, and analyzed by Statistical Package for Social Sciences version 25. Bivariate binary logistic regression was used to select candidate variables with p < 0.25. Multicollinearity was checked by using the variance inflation factor and it was less than 10. Model adequacy was checked by Hosmer & Lemeshow goodness of test (p > 0.05). In the multivariable binary logistic regression, the association between outcome and independent variables was declared at p < 0.05 with its adjusted odds ratio (AOR) at a 95% confidence level.

Results
The prevalence of PTSD among the respondents was 67.5% (95% CI: 63–72). Being a merchant (AOR = 0.41 [95% CI: 0.02–0.85]), witnessing the destruction of property (AOR = 1.67 [95% CI: 1.01–2.74]), facing trauma during displacement (AOR = 6.00 [95% CI: 2.75–13.10]), frequency of displacement (AOR = 0.31 [95% CI: 0.11–0.85]), being distressed (AOR = 5.42 [95% CI: 3.25–9.05]), and unemployment (AOR = 2.09 [95% CI: 1.24–3.54]) were factors significantly associated with PTSD.

Conclusion
This study provides evidence of the high prevalence of PTSD among internally displaced people. Therefore, mental health and psychosocial support are urgently required to address the identified factors and help the displaced people against long-term avoidable suffering.
What roles does physical activity play following the death of a parent as a young person? A qualitative investigation
Authors: Williams Jane , Howlett Neil , Shorter Gillian W. , Zakrzewski-Fruer Julia K. , Chater Angel Marie 
Published: January 2023

Abstract
Background
Physical activity benefits physical and mental health. However, limited research investigates if physical activity can improve outcomes from the grieving process following the death of a parent.

Methods
Semi-structured interviews were conducted with 14 individuals (n = 8 female; age M = 31.2 years), who had experienced the death of a parent when they were aged between 10 and 24 years old, using retrospective recall. Data were analysed inductively using thematic analysis.

Results
Six themes were identified. Physical activity was seen as; 1) ‘Therapeutic’; providing an 2) ‘Emotional Outlet’ and created a strong sense of 3) ‘Social Support’. Alongside it 4) ‘Builds Confidence’, and led to 5) ‘Finding Yourself’ and 6) ‘Improved Health and wellbeing’ (physical and psychological).

Conclusion
Physical activity has the potential to provide positive experiences following a parental bereavement. It can provide a sense of freedom and was seen to alleviate grief outcomes, build resilience, enable social support and create a stronger sense of self. Bereavement support services for young people who have experienced death of a parent should consider physical activity as a viable intervention to support the grieving process.