bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Assembly, from Practice to Theory: Safe, Complete and
Linear-Time
Authors: Cairo Massimo , Rizzi Romeo , Tomescu Alexandru I. , Zirondelli Elia C. 
Published: November 2023

Genome assembly asks to reconstruct an unknown string from many shorter substrings of it. Even though it is one of the key problems in Bioinformatics, it is generally lacking major theoretical advances. Its hardness stems both from practical issues (size and errors of real data), and from the fact that problem formulations inherently admit multiple solutions. Given these, at their core, most state-of-the-art assemblers are based on finding non-branching paths (
unitigs
) in an assembly graph. While such paths constitute only partial assemblies, they are likely to be correct. More precisely, if one defines a genome assembly solution as a
closed arc-covering walk
of the graph, then unitigs appear in all solutions, being thus
safe
partial solutions. Until recently, it was open what are
all
the safe walks of an assembly graph. Tomescu and Medvedev (RECOMB 2016) characterized all such safe walks (
omnitigs
), thus giving the first safe and
complete
genome assembly algorithm. Even though maximal omnitig finding was later improved to quadratic time by Cairo et al. (ACM Trans. Algorithms 2019), it remained open whether the crucial linear-time feature of finding unitigs can be attained with omnitigs.

We answer this question affirmatively, by describing a surprising
O(m)
-time algorithm to
identify
all maximal omnitigs of a graph with
n
nodes and
m
arcs, notwithstanding the existence of families of graphs with
Θ (mn)
total maximal omnitig size. This is based on the discovery of a family of walks (
macrotigs
) with the property that all the non-trivial omnitigs are univocal extensions of subwalks of a macrotig. This has two consequences: (1) A
linear-time output-sensitive
algorithm enumerating all maximal omnitigs. (2) A

compact
O(m)
representation

of all maximal omnitigs, which allows, e.g., for
O(m)
-time computation of various statistics on them. Our results close a long-standing theoretical question inspired by practical genome assemblers, originating with the use of unitigs in 1995. We envision our results to be at the core of a reverse transfer from theory to practical and
complete
genome assembly programs, as has been the case for other key Bioinformatics problems.
Impact of Rare Structural Variant Events in Newly Diagnosed Multiple Myeloma
Authors: Chojnacka Monika , Diamond Benjamin , Ziccheddu Bachisio , Rustad Even , Maclachlan Kylee , Papadimitriou Marios , Boyle Eileen M. , Blaney Patrick , Usmani Saad , Morgan Gareth , Landgren Ola , Maura Francesco 
Published: November 2023

Abstract

Purpose:
Whole-genome sequencing (WGS) of patients with newly diagnosed multiple myeloma (NDMM) has shown recurrent structural variant (SV) involvement in distinct regions of the genome (i.e., hotspots) and causing recurrent copy-number alterations. Together with canonical immunoglobulin translocations, these SVs are recognized as “recurrent SVs.” More than half of SVs were not involved in recurrent events. The significance of these “rare SVs” has not been previously examined.

Experimental Design:
In this study, we utilize 752 WGS and 591 RNA sequencing data from patients with NDMM to determine the role of rare SVs in myeloma pathogenesis.

Results:
Ninety-four percent of patients harbored at least one rare SV event. Rare SVs showed an SV class-specific enrichment within genes and superenhancers associated with outlier gene expression. Furthermore, known myeloma driver genes recurrently impacted by point mutations were dysregulated by rare SVs.

Conclusions:
Overall, we demonstrate the association of rare SVs with aberrant gene expression supporting a potential driver role in myeloma pathogenesis.
Targeted Radiation Delivery before Haploidentical HCT for High-risk Leukemia or MDS Patients Yields Long-term Survivors
Authors: Orozco Johnnie J. , Vo Phuong T. , Gooley Ted A. , Haaf Robyn L. , Lundberg Sally J. , Hamlin Donald K. , Wilbur D. Scott , Matesan Manuela C. , Fisher Darrell R. , Gopal Ajay K. , Green Damian J. , Pagel John M. , Sandmaier Brenda M. 
Published: November 2023

Abstract

Purpose:
Hematopoietic cell transplantation (HCT) has curative potential for myeloid malignancies, though many patients cannot tolerate myeloablative conditioning with high-dose chemotherapy alone or with total-body irradiation (TBI). Here we report long-term outcomes from a phase I/II study using iodine-131 (131I)-anti-CD45 antibody BC8 combined with nonmyeloablative conditioning prior to HLA-haploidentical HCT in adults with high-risk relapsed/ refractory acute myeloid or lymphoid leukemia (AML or ALL), or myelodysplastic syndrome (MDS; ClinicalTrials.gov, NCT00589316).

Patients and Methods:
Patients received a tracer diagnostic dose before a therapeutic infusion of 131I­anti-CD45 to deliver escalating doses (12–26 Gy) to the dose-limiting organ. Patients subsequently received fludarabine, cyclophosphamide (CY), and 2 Gy TBI conditioning before haploidentical marrow HCT. GVHD prophylaxis was posttransplant CY plus tacrolimus and mycophenolate mofetil.

Results:
Twenty-five patients (20 with AML, 4 ALL and 1 high-risk MDS) were treated; 8 had ≥ 5% blasts by morphology (range 9%–20%), and 7 had previously failed HCT. All 25 patients achieved a morphologic remission 28 days after HCT, with only 2 patients showing minimal residual disease (0.002–1.8%) by flow cytometry. Median time to engraftment was 15 days for neutrophils and 23 days for platelets. Point estimates for overall survival and progression-free survival were 40% and 32% at 1 year, and 24% at 2 years, respectively. Point estimates of relapse and nonrelapse mortality at 1 year were 56% and 12%, respectively.

Conclusions:
131I-anti-CD45 radioimmunotherapy prior to haploidentical HCT is feasible and can be curative in some patients, including those with disease, without additional toxicity.
PASTA: A Dataset for Modeling PArticipant STAtes in Narratives
Authors: Ghosh Sayontan , Koupaee Mahnaz , Chen Isabella , Ferraro Francis , Chambers Nathanael , Balasubramanian Niranjan 
Published: November 2023

Abstract
The events in a narrative are understood as a coherent whole via the underlying states of their participants. Often, these participant states are not explicitly mentioned, instead left to be inferred by the reader. A model that understands narratives should likewise infer these implicit states, and even reason about the impact of changes to these states on the narrative. To facilitate this goal, we introduce a new crowdsourced English-language, Participant States dataset, PASTA. This dataset contains inferable participant states; a counterfactual perturbation to each state; and the changes to the story that would be necessary if the counterfactual were true. We introduce three state-based reasoning tasks that test for the ability to infer when a state is entailed by a story, to revise a story conditioned on a counterfactual state, and to explain the most likely state change given a revised story. Experiments show that today’s LLMs can reason about states to some degree, but there is large room for improvement, especially in problems requiring access and ability to reason with diverse types of knowledge (e.g., physical, numerical, factual).1
An Investigation into the Relationship between Diaspora and Identity with Reference to the Iranian Diaspora
Authors: Amrollahi Mohammed Taghi , Saeidabadi Mohammad Reza 
Published: November 2023

Abstract
The purpose of this article is to examine the relationship between diaspora and identity with reference to the Iranian diaspora as a case study. Although there has been a recent growth in the study of ideational factors and their effects on sociopolitical issues, identity remains understudied within the mainstream literature on diaspora studies, international relations (IR) and foreign policy analysis (FPA). The aim is to challenge the purely realist and power-based explanations that have dominated the discourse by introducing the notion of identity and exploring it in relation to the Iranian diaspora. The paper’s novel approach lies in its categorisation of Iranian diaspora identity into three main components: nationalist (ancient Iran) tendencies, religious (Islamic-Shiite) tendencies and secular (Western) tendencies. The identity components of Iranians abroad and their interaction with the homeland are relatively comparable to those of their compatriots at home, showing intersecting areas of commonality and difference.
Humanising research relationships: Democratising education-based enquiry with student researchers
Authors: Green Matthew , Little Alice , Dobson Elliot , Glover Oscar , Patterson Joshua 
Published: November 2023

This paper critically reflects upon the experiences of three student researchers during a participatory research project conducted in an English sixth-form academy. Discussion is centred upon a research conversation involving three student researchers (aged 17 years) and two postgraduate researchers, from York St John University, UK. Collectively, critical insights are offered into the process of conducting education-based participatory research; leading to the identification of situations in which ethical challenges, tensions and power imbalances arose. Through reflection, attention is paid to how researchers can disrupt neoliberal educational agendas and create opportunities for democratic research. The narratives presented in this paper offer recommendations for facilitating more democratic research relationships, that centralise the valuing of all voices and promote collaborative approaches to research. Envisioning this ‘space’ for future research through adaptation of Freire's ‘culture circles’, the article concludes with suggestions of how researchers may work to humanise research relationships.
Is nurses’ clinical competence associated with their moral identity and injury?
Authors: Teng Yue , Dehghan Mahlagha , Hossini Rafsanjanipoor Sayed Mortaza , Altwalbeh Diala , Riyahi Zahra , Farahmandnia Hojjat , Zeidabadi Ali , Zakeri Mohammad Ali 
Published: November 2023

Background The enhancement of nursing care quality is closely related to the clinical competence of nurses, making it a crucial component within health systems. Objective The present study investigated the relationship between nurses’ clinical competence, moral identity, and moral injury during the COVID-19 outbreak. Research design This cross-sectional study was carried out among frontline nurses, using the Moral Identity Questionnaire (MIQ), the Moral Injury Symptom Scale-Healthcare Professionals version (MISS-HP), and the Competency Inventory for Registered Nurse (CIRN) as data collection tools. Participants and research context: The research population for this study consisted of all frontline nurses ( n = 251) employed in a hospital in southern Iran. Sampling was conducted between May 1, 2021 and September 30, 2021, during the COVID-19 outbreak. Ethical considerations The present study received approval from the research ethics committee of Rafsanjan University of Medical Sciences, with project No. 99267 and code of ethics ID No. IR. RUMS.REC.1399.262, dated 15.02.2021. Results According to the study findings, 42.2% of the nurses demonstrated high clinical competence, while 51.4% exhibited moderate clinical competence. The results indicated a positive correlation between moral identity and clinical competence but a negative correlation between moral injury and clinical competence. Furthermore, the variables of moral identity and moral injury were found to predict 10% of the variance in clinical competence. Conclusion According to the results, moral identity and moral injury had an impact on the clinical competence of nurses. Therefore, implementing a program aimed at enhancing moral identity and providing training strategies to address moral injury during crises like the COVID-19 pandemic can lead to improvements in nurses’ clinical competence and the overall quality of care they provide.
Toxicological Assessment of Higher Olefins in OECD TG 422 Repeated Dose and Reproductive /Developmental Toxicity Screening Tests in Han Wistar Rats
Authors: Shi Quan , Carrillo Juan-Carlos , Penman Michael G. , Shen Hua , North Colin M. , Jia Sophie , Borsboom-Patel Tilly , Tian Yuan , Hubert Fabienne , Manton Jason C. , Boogaard Peter J. 
Published: November 2023

Higher olefins (HO) are used primarily as intermediates in the production of other chemicals, such as polymers, fatty acids, plasticizer alcohols, surfactants, lubricants, amine oxides, and detergent alcohols. The potential toxicity of five HO (i.e., 1-Octene, Nonene, Decene, Hexadecene, and 1-Octadecene) with carbon ranging from C8 to C18 was examined in a combined repeated dose and reproduction/developmental toxicity screening study (OECD TG 422). These five HO were administered to Han Wistar rats by gavage at 0 (controls), 100, 300, and 1000 mg/kg bw/day. As a group of substances, adaptive changes in the liver (liver weight increase without pathological evidence), as well as increased kidney weight in male rats, were observed in HO with carbon numbers from C8 to C10. The overall systemic no observed adverse effect level (NOAEL) for all HO was determined at 1000 mg/kg bw/day. In the reproductive/developmental toxicity assessment, offspring viability, size, and weights were reduced in litters from females treated with Nonene at 1000 mg/kg bw/day. The overall no observed effects level (NOEL) for reproductive toxicity was considered to be 300 mg/kg bw/day for Nonene and 1000 mg/kg bw/day for the other four HO, respectively. These data significantly enrich the database on the toxicity of linear and branched HO, allowing comparison with similar data published on a range of linear and branched HO. Comparisons between structural class and study outcome provide further supportive data in order to validate the read-across hypothesis as part of an overall holistic testing strategy.
Intact peritoneum in a child with ileal perforation from a firearm injury
Authors: Ali Syed Waqas , Jahan Yaqoot , Anwar Farah , Khalid Saad , Khan Muhammad Arif Mateen 
Published: November 2023

Introduction Indirect intra-abdominal injury with an intact peritoneum following close passage of highly energized projectiles is an uncommon but clearly described phenomenon; likewise delayed gastrointestinal perforation hours or days after passage of a high-energy stress wave from primary blast injury is uncommon. Awareness of these two rare occurrences is required to ensure delayed perforations are diagnosed and managed in a timely manner. Case report An 8-year-old male child sustained a shotgun injury to the right elbow and the abdominal wall only of the right hypochondrium. Due to a non-salvageable joint injury, he underwent amputation of the right upper limb above the elbow, but on the third day of admission, he developed peritonitis and an X-ray revealed pneumoperitoneum. On abdominal exploration, two small ileal perforations were found without penetration of the peritoneum or diaphragm. The ileal injuries were primarily repaired and the postoperative course was uneventful. Conclusion Indirect injury to abdominal viscera from the primary blast effect of close passage of high-energy projectiles resulting is rare and can have significant consequences if not diagnosed and managed early.
Sex-Specific Morphometric Analysis of Ascending Aorta and Aortic Arch for Planning Thoracic Endovascular Aortic Repair: A Retrospective Cohort Study
Authors: Katsarou Maria , Mandigers Tim J. , Berczeli Marton , Mujeeb Zubair M. , Belvroy Viony M. , Bissacco Daniele , van Herwaarden Joost A. , Trimarchi Santi , Bismuth Jean 
Published: November 2023

Objective: In many studies on aortic disease, women are underrepresented. The present study aims to assess sex-specific morphometric differences and gain more insight into endovascular treatment of the ascending aorta (AA) and arch. Methods: Electrocardiogram-gated cardiac computed tomography scans of 116 consecutive patients who were evaluated for transcatheter aortic valve replacement were retrospectively reviewed. Measurements of the AA and aortic arch were made in multiplanar views, perpendicular to the semi-automatic centerline. Multiple linear regression analysis was performed to identify predictors affecting AA and aortic arch diameter in men and women. Propensity score matching was used to investigate whether sex influences aortic morphology. Results: In both sexes, body surface area (BSA) was identified as a positive predictor and diabetes as a negative predictor for aortic diameters. In men, age was identified as a positive predictor and smoking as a negative predictor for aortic diameters. Propensity score matching identified 40 pairs. Systolic and diastolic mean diameters and AA length were significantly wider in men. On average, male aortas were 7.4% wider than female aortas, both in systole and diastole. Conclusions: The present analysis demonstrates that, in women, increased BSA is associated with increased aortic arch diameters, while diabetes is associated with decreased AA and arch diameters. In men, increased BSA and age are associated with increased AA and arch diameters, while smoking and diabetes are associated with decreased AA and arch diameters. Men were confirmed to have 7.4% greater AA and arch diameters than women. Clinical Impact Men had 7.4% greater ascending aorta and arch diameters than women in a retrospective cohort, gated computed tomography-based study of 116 patients. Sex-specific differences in ascending aortic and arch size should be considered by aortic endovascular device manufacturers and physicians when developing ascending and arch endografts and planning aortic interventions.
Preoperative Education Prior to Hip or Knee Arthroplasty Is Associated With Home Discharge but Not Reduced Length of Stay
Authors: Brossier Monika , Schwartz-Dillard Jessica , McInerney Danielle , Smith Jerome Brent , Nguyen Joseph , Murray-Weir Mary , Edwards Danielle 
Published: November 2023

Background: Increasing numbers of patients are undergoing total joint arthroplasty as a treatment for osteoarthritis, which can be an anxiety-provoking experience. Setting expectations through a preoperative physical therapy (pre-op PT) session can alleviate some of these stressors, potentially decrease hospital length of stay (LOS), and promote home discharge. Purpose: We sought to determine whether attending a pre-op PT session is associated with decreased hospital LOS and home discharge in total hip arthroplasty (THA) and total knee arthroplasty (TKA) patients. Methods: A retrospective cohort study was performed of 20,822 patients who underwent THA or TKA between January 2020 and December 2023. Pre-op PT attendance and covariates, including patient demographics and clinical data, were collected and analyzed for association with LOS and discharge disposition. Results: Unadjusted univariate analysis revealed that THA and TKA patients who received pre-op PT had a significantly lower average LOS and were more likely to be discharged home. Our multivariate regression model showed that pre-op PT was not significantly associated with LOS in both groups but was significantly associated with home discharge among THA patients. Conclusions: Our retrospective study of the effect of pre-op PT education on LOS and discharge disposition for elective THA and TKA patients found different results in univariate and multivariate analysis. Further study is needed to confirm the association found on multivariate analysis between pre-op PT and home discharge in THA patients.
Dichotomous grouping of peripheral arterial calcification grades: A practical predictor of outcome after endovascular therapy in peripheral arterial disease
Authors: Aboloyoun Hesham , Zaki Hazem Mohamed , Hasaballa Ayman , Elbadawy Ahmed 
Published: November 2023

Background There is a general agreement that arterial calcification affects the results of endovascular therapy for peripheral arterial disease (PAD). In addition to lacking evidence for their impact, existing calcification scores are complex, and not practical in everyday decision making. The global limb anatomic staging system (GLASS) adopted dichotomous grouping of calcification grades. Objective In this study we aim to investigate the impact of peripheral arterial calcification scoring after dichotomous grouping on midterm outcomes following endovascular therapy for PAD. Methods This prospective study included all consecutive patients with PAD indicated for endovascular therapy procedure who presented to our tertiary referral center in the period between October 2020 and October 2021. Patients were grouped into Group A ( n = 40): with no-to mild calcification (PACSS grade 0,1 and 2), and Group B ( n = 53): with severe calcification (PACSS grades 3 and 4). Primary endpoints included technical success rate, primary patency rates, and major adverse limb events rate (MALE) during 2 years of follow-up. Results The mean age of the studied cases ( n = 93) was 59.31 ± 6.46 years (range 50–75). 70 patients (75.3%) were males, and 23 (24.7%) were females. There was no statistically significant difference between the two groups regarding technical success rate (97.5% in group A versus 94.33% in Group B, p = .457). The Primary patency rate after 1 year was lower in group B (74%) compared to group A (89.7%), but this difference was not statistically significant ( p = .059). However, the 2-year primary patency rate was significantly lower in group B compared to group A (64% versus 84.6% respectively, p = .034). MALE rate after 2 years was significantly higher in group B (28%) as compared to group A (10.4%), P = .048. Studying suspected risk factors revealed that severe calcification was more common in patients with ischemic heart disease (34%) and chronic kidney disease (11%), P= .003 and .002 respectively. Logistic regression analysis showed that patients suffered from IHD and those with length of lesion ≥ 5 cm are about five times more likely to have severe calcification compared to their counterparts (OR = 4.875, 95%CI = 1.293–18.383, p = .019, and OR = 4.513, 95% CI = 11.138–17.893, p = .032), respectively. Conclusion The presence of severe calcification is associated with significantly lower midterm primary patency rates and higher rate of major adverse limb events after endovascular intervention for lower limb denovo arterial lesions.