bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new disjunctive literal insertion fault detection strategy in boolean specifications
Authors: Paul T. K. , Chowdhury M. J. M. , Lau M. F. 
Published: February 2021

AbstractIn fault‐based Boolean expression testing, the main challenge is to generate effective test cases that can detect faults within expressions. Previous studies show that it is hard to detect literal insertion faults, more specifically Disjunctive literal insertion fault (LIF[+]) compared with other faults in Boolean expressions. Researchers have been using different strategies such as multiple near false point coverage (MNFP) and modified condition decision coverage (MCDC) to detect LIF[+] faults. However, these strategies have their own limitations. For example, MNFP can only be applied when the expression is in irredundant disjunctive normal form (IDNF), and MCDC detects a low percentage of LIF[+] faults. In this paper, we propose an abstract syntax tree (AST)‐based test case generation strategy for LIF[+] fault detection that overcomes these limitations. Furthermore, our experimental results indicate that, on average, the test suites satisfying the proposed strategy can detect approximately 97.3% of LIF[+] faults for general form expressions and 89.7% of LIF[+] faults for IDNF expressions, which are 15.6% and 13.8% improvement, respectively, compared to the MCDC test suites. Moreover, the size of the required test suite is smaller than that of MCDC test suite.
Analysis of the primary sources of quantitative adult plant resistance to stripe rust in U.S. soft red winter wheat germplasm
Authors: Ward Brian P. , Merrill Keith , Bulli Peter , Pumphrey Mike , Mason Richard Esten , Mergoum Mohamed , Johnson Jerry , Sapkota Suraj , Lopez Benjamin , Marshall David , Brown‐Guedira Gina 
Published: February 2021

AbstractStripe rust, or yellow rust (Puccinia striiformis Westend. f. sp. tritic), is a disease of wheat (Triticum aestivum L.) historically causing significant economic losses in cooler growing regions. Novel isolates of stripe rust with increased tolerance for high temperatures were detected in the United States circa 2000. This increased heat tolerance puts geographic regions, such as the soft red winter wheat (SRWW) growing region of the southeastern United States, at greater risk of stripe rust induced losses. In order to identify sources of stripe rust resistance in contemporary germplasm, we conducted genome‐wide association (GWA) studies on stripe rust severity measured in two panels. The first consisted of 273 older varieties, landraces, and some modern elite breeding lines and was evaluated in environments in the U.S. Pacific Northwest and the southeastern United States. The second panel consisted of 588 modern, elite SRWW breeding lines and was evaluated in four environments in Arkansas and Georgia. The analyses identified three major resistance loci on chromosomes: 2AS (presumably the 2NS:2AS alien introgression from Aegilops ventricosa Tausch; syn. Ae. caudata L.), 3BS, and 4BL. The 4BL locus explained a greater portion of variance in resistance than either the 2AS or 3BS loci in southeastern environments. However, its effects were unstable across different environments and sets of germplasm, possibly a result of its involvement in epistatic interactions. Relatively few lines carry resistance alleles at all three loci, suggesting that there is a pre‐existing reservoir of enhanced stripe rust resistance that may be further exploited by regional breeding programs.
The controversial debate on the role of water reservoirs in reducing water scarcity
Authors: Kellner Elke 
Published: February 2021

AbstractReservoirs are built worldwide for a higher water supply in dry periods by storing water temporarily in wet periods. Recent socio‐hydrology studies hypothesized, by creating “supply–demand cycles”, that reservoirs can lead indirectly to counterintuitive dynamics such as more water scarcity and a higher economic and social vulnerability. This opinion argues that reservoirs are part of co‐evolutionary processes with natural, social, and engineered elements and therefore, water scarcity need to be analyzed within socio‐political interactions. Aspects such as (a) institutions; (b) governance processes; (c) social–ecological factors; (d) narratives of water scarcity; and (e) powerful economic interests are essential to understand feedback mechanisms between reservoirs and water scarcity and to hypothesize long‐term phenomena such as water scarcity. Neglecting these interactions could lead to biased research agendas, misleading conclusions, and adverse effects on the transformation process toward sustainability. Given the complexity of social–ecological systems, the diversity and critical capacity of inter‐ and transdisciplinary work is crucial to further advance the study of unintended side effects of reservoirs or — more general — the study of socio‐hydrology.This article is categorized under:
Human Water
Uncovering targets of the Leader protease: Linking RNA‐mediated pathways and antiviral defense
Authors: Saiz Margarita , Martinez‐Salas Encarnacion 
Published: February 2021

AbstractRNA viruses have developed specialized mechanisms to subvert host RNA‐binding proteins (RBPs) favoring their own gene expression. The Leader (L) protein of foot‐and‐mouth disease virus, a member of the Picornaviridae family, is a papain‐like cysteine protease that self‐cleaves from the polyprotein. Early in infection, the L protease cleaves the translation initiation factors eIF4GI and eIF4GII, inducing the shutdown of cap‐dependent translation. However, the cleavage sites on the viral polyprotein, eIF4GI, and eIF4GII differ in sequence, challenging the definition of a consensus site for L targets. Identification of Gemin5 and Daxx proteolytic products in infected cells unveiled a motif centered on the RKAR sequence. The RBP Gemin5 is a member of the survival of motor neurons complex, a ribosome interacting protein, and a translation downregulator. Likewise, the Fas‐ligand Daxx is a multifunctional adaptor that plays key roles in transcription control, apoptosis, and innate immune antiviral response. Remarkably, the cleavage site on the RNA helicases MDA5 and LGP2, two relevant immune sensors of the retinoic acid‐inducible gene‐I (RIG‐I)‐like receptors family, resembles the L target site of Gemin5 and Daxx, and similar cleavage sites have been reported in ISG15 and TBK1, two proteins involved in type I interferon response and signaling pathway, respectively. In this review we dissect the features of the L cleavage sites in essential RBPs, eventually helping in the discovery of novel L targets.This article is categorized under:
RNA in Disease and Development > RNA in Disease
Translation > Translation Regulation
Cross‐talk between autophagy and sporulation in Saccharomyces cerevisiae
Authors: Barve Gaurav , Manjithaya Ravi 
Published: February 2021

AbstractUnicellular organisms, like yeast, have developed mechanisms to overcome environmental stress conditions like nutrient starvation. Autophagy and sporulation are two such mechanisms employed by yeast cells. Autophagy is a well‐conserved, catabolic process that degrades excess and unwanted cytoplasmic materials and provides building blocks during starvation conditions. Thus, autophagy maintains cellular homeostasis at basal conditions and acts as a survival mechanism during stress conditions. Sporulation is an essential process that, like autophagy, is triggered due to stress conditions in yeast. It involves the formation of ascospores that protect the yeast cells during extreme conditions and germinate when the conditions are favorable. Studies show that autophagy is required for the sporulation process in yeast. However, the exact mechanism of action is not clear. Furthermore, several of the core autophagy gene knockouts do not sporulate and at what stage of sporulation they are involved is not clear. Besides, many overlapping proteins function in both sporulation and autophagy and it is unclear how the pathway‐specific roles of these proteins are determined. All these observations suggest that the two processes cross‐talk. Individually, some key features from both the processes remain to be studied with respect to the source of membrane for autophagosomes, prospore membrane (PSM) formation, and closure of the membranes. Therefore, it becomes crucial to study the cross‐talk between autophagy and sporulation. In this review, the cross‐talk between the two pathways, the common protein machineries have been discussed.
Tracking and Traceability
Authors: Van der Gouw Lex 
Published: February 2021

AbstractThe ability to trace a cellular product from donor to patient and vice versa is essential for the patient’s safety. Uniform product description as well as standardization of product labelling is necessary to ensure adequate tracking and tracing of cellular products.Also, with the increasing use of automated systems, accurate and unambiguous electronic transfer of product information is critical.Standardization comprises several elements which together will form an ‘information environment’. Together with electronic standards such as ISBT128 and Eurocode, this will further enhance safety, accuracy and efficiency in tracking and tracing cellular products.
Document Development, Implementation, Review, Archive, and Disposal
Authors: van Sinderen Nick 
Published: February 2021

AbstractThe challenges in setting up a document management system are both technical and organizational. Both need to be addressed to achieve success. Time is required to make a thorough inventory of system requirements, whether electronic or paper-based, and to organize the team that will maintain the system. It is crucial that key stakeholders are involved from the beginning and that they see the value of the quality system in improving clinical care. Routine use by all staff will prevent it from being seen as a burdensome additional imposition due to the need for JACIE accreditation. When fully implemented, the documents and policies become a readily accessible, clinically relevant, educational resource that improves patient care.
Qualification and Validation
Authors: Monteleone Renza , Klarmann Dieter 
Published: February 2021

AbstractQualification and validation are integral components of the quality risk management system. Decisions about the scope and extent of qualification and validation should be based on detailed and documented risk assessments performed by the key transplant program personnel (collection/processing/clinical) who are responsible for critical aspects of the relevant operations over the life cycle of the product or process.
Outcome Analysis
Authors: Emmett Anne 
Published: February 2021

AbstractTo understand and hence improve the positive impact of any healthcare activity, procedure or intervention, it is essential that there is an objective analysis of the activity, procedure or intervention based on predetermined standards.In the field of haematopoietic stem cell transplantation, outcome analysis is the process by which the results of a transplant procedure are formally assessed. It includes a series of reviews for evaluating the effectiveness of the health care provided and for identifying the most promising therapies and transplant approaches, given the available medical evidence and healthcare resources.Outcome analysis allows the transplant team to understand the effects of their practice and improve quality. Its relevance is due to transplant involving high treatment-related risk, significant practice variations, and continual practice developments – for example, recent developments in CAR-T and IEC therapies.The main aim of this chapter is to discuss how to find outcome data and how and when to present it. This will need to be adapted to the local programme.
Personnel Requirements Including Job Descriptions
Authors: Tepebasi Songul , Kozanoglu Ilknur 
Published: February 2021

AbstractPersonnel are one of the most important parts of the quality management system within any haematopoietic stem cell transplantation and cellular therapy programme. Two main steps establish the quality management activities in relation to personnel. The first step is the creation of a well-defined organisational chart; the second step is the appointment of the correct employee for the correct job and responsibilities, with opportunities for continuous development of their competencies. Job descriptions for personnel should not be limiting and should support continuous professional development. In addition, accurate and frequent communication will increase cooperation within cellular therapy centres, minimise margins of error and contribute positively to patient care.
Eigenbranes in Jackiw-Teitelboim gravity
Authors: Blommaert Andreas , Mertens Thomas G. , Verschelde Henri 
Published: February 2021

Abstract
It was proven recently that JT gravity can be defined as an ensemble of L × L Hermitian matrices. We point out that the eigenvalues of the matrix correspond in JT gravity to FZZT-type boundaries on which spacetimes can end. We then investigate an ensemble of matrices with 1 ≪ N ≪ L eigenvalues held fixed. This corresponds to a version of JT gravity which includes N FZZT type boundaries in the path integral contour and which is found to emulate a discrete quantum chaotic system. In particular this version of JT gravity can capture the behavior of finite-volume holographic correlators at late times, including erratic oscillations.
Completeness and complementarity for μ → eγ, μ → $$ e\overline{e}e $$ and μA → eA
Authors: Davidson S. 
Published: February 2021

Abstract
Lepton Flavour Violation (LFV) is New Physics that must occur, but is stringently constrained by experiments searching for μ ↔ e flavour change, such as μ → eγ, μ →$$ e\overline{e}e $$
e

e
¯

e
or μ → e conversion. However, in an Effective Field Theory(EFT) parametrisation, there are many more μ ↔ e operators than restrictive constraints, so determining operator coefficients from data is a remote dream. It is nonetheless interesting to learn about New Physics from data, so this manuscript introduces “observable-vectors” in the space of operator coefficients, which identify at any scale the combination of coefficients probed by the observable. These vectors have an overlap ≳ 10−3 with most of the coefficients, and are used to study whether μ → eγ, μ →$$ e\overline{e}e $$
e

e
¯

e
and μ → e conversion give complementary information about New Physics. The appendix gives updated sensitivities of these processes, (and a subset of τ → ℓ decays), to operator coefficients at the weak scale in the SMEFT and in the EFT below mW.
Stability Estimates for Phase Retrieval from Discrete Gabor Measurements
Authors: Alaifari Rima , Wellershoff Matthias 
Published: February 2021

AbstractPhase retrieval refers to the problem of recovering some signal (which is often modelled as an element of a Hilbert space) from phaseless measurements. It has been shown that in the deterministic setting phase retrieval from frame coefficients is always unstable in infinite-dimensional Hilbert spaces (Cahill et al. in Trans Am Math Soc Ser B 3(3):63–76, 2016) and possibly severely ill-conditioned in finite-dimensional Hilbert spaces (Cahill et al. in Trans Am Math Soc Ser B 3(3):63–76, 2016). Recently, it has also been shown that phase retrieval from measurements induced by the Gabor transform with Gaussian window function is stable under a more relaxed semi-global phase recovery regime based on atoll functions (Alaifari in Found Comput Math 19(4):869–900, 2019). In finite dimensions, we present first evidence that this semi-global reconstruction regime allows one to do phase retrieval from measurements of bandlimited signals induced by the discrete Gabor transform in such a way that the corresponding stability constant only scales like a low order polynomial in the space dimension. To this end, we utilise reconstruction formulae which have become common tools in recent years (Bojarovska and Flinth in J Fourier Anal Appl 22(3):542–567, 2016; Eldar et al. in IEEE Signal Process Lett 22(5):638–642, 2014; Li et al. in IEEE Signal Process Lett 24(4):372–376, 2017; Nawab et al. in IEEE Trans Acoust Speech Signal Process 31(4):986–998, 1983).
Fine mapping of a thrips resistance QTL in Capsicum and the role of diterpene glycosides in the underlying mechanism
Authors: van Haperen Pauline , Voorrips Roeland E. , van Kaauwen Martijn , van Eekelen Henriëtte D. L. M. , de Vos Ric C. H. , van Loon Joop J. A. , Vosman Ben 
Published: February 2021

AbstractKey messageA major thrips resistance QTL inCapsicumwas fine-mapped to a region of 0.4 Mbp, and a multidisciplinary approach has been used to study putative underlying mechanisms.AbstractResistance to thrips is an important trait for pepper growers. These insects can cause extensive damage to fruits, flowers and leaves on field and greenhouse grown plants worldwide. Two independent studies inCapsicumidentified diterpene glycosides as metabolites that are correlated with thrips resistance. In this study, we fine-mapped a previously defined thrips resistance QTL on chromosome 6, to a region of 0.4 Mbp harbouring 15 genes. Two of these 15 candidate genes showed differences in gene expression upon thrips induction, when comparing plants carrying the resistance allele in homozygous state to plants with the susceptibility allele in homozygous state for the QTL region. Three genes, including the two genes that showed difference in gene expression, contained a SNP that was predicted to lead to changes in protein structure. Therefore, these three genes, i.e. an acid phosphatase 1 (APS1), an organic cation/carnitine transporter 7 (OCT7) and an uncharacterized locus LOC107874801, are the most likely candidates for playing a role in thrips resistance and are a first step in elucidating the genetic basis of thrips resistance inCapsicum. In addition, we show that the diterpene glycoside profiles did not differ between plants with the resistance and susceptibility allele for the chromosome 6 QTL, suggesting that these compounds do not play a role in the resistance conferred by the genes located in the major thrips resistance QTL studied.
The bone microstructure from anterior cruciate ligament footprints is similar after ligament reconstruction and does not affect long-term outcomes
Authors: Stolarz Mateusz , Rajca Jolanta , Cyganik Paulina , Karpe Jacek , Wrobel Zygmunt , Binkowski Marcin , Humpa Filip , Janik Małgorzata , Czyzewski Damian , Kwiatkowski Zbigniew , Ficek Krzysztof 
Published: February 2021

Abstract
Purpose
The purpose of this study was to assess the quality of the bone tissue microstructure from the footprints of the anterior cruciate ligament (ACL) and its impact on late follow-up outcomes in patients who undergo anterior cruciate ligament reconstruction (ACLR).

Methods
The records of 26 patients diagnosed with a completely torn ACL who underwent ACLR were collected. During the surgery performed using the Felmet method, bone blocks from the native ACL footprints were collected. The primary measurements of the bone microstructure were made using a microtomographic scanner. In late follow-up examinations, a GNRB arthrometer was used.

Results
There was no significant difference in the bone microstructure assessed using micro-CT histomorphometric data according to the blood test results, plain radiographs, age or anthropometric data. There was no difference in the bone volume/total volume ratio or trabecular thickness in the area of the native ACL footprints. Routine preoperative examinations were not relevant to the quality of the bone microstructure. The elapsed time from an ACL injury to surgery had no relevance to the results of arthrometry.

Conclusion
The similarities in the microstructure of bone blocks from ACL footprints from the femur and tibia allow the variable use of these blocks to stabilize grafts in the Felmet method. The bone microstructure is not dependent on the time from injury to surgery. Histomorphometric values of the structure of the femoral and tibial ACL footprints have no impact on the long-term stability of the operated knee joint.

Trial registration
The approval of the Bioethics Committee of the Silesian Medical Chamber in Katowice, Poland (resolution 16/2014) was given for this research.

Level of evidence
II.
Safety profile of chimeric antigen receptor T-cell immunotherapies (CAR-T) in clinical practice
Authors: Bonaldo Giulia , Montanaro Nicola , AlbertoVaccheri  , Motola Domenico 
Published: February 2021

Abstract
Purpose
Two chimeric antigen receptor T-cell (CAR-T) therapies have been approved in the United States (USA) in 2017 and Europe (EU) in 2018: axicabtagene ciloleucel and tisagenlecleucel. They contain the patient’s own T cells, which are extracted, genetically modified, and reinfused. Alongside the good efficacy results, the assessment of safety profile of these new therapies represents a great challenge. Our aim was to analyze the reports of the adverse drug reactions (ADR) after CAR-T administration as occurred in the real clinical setting.

Methods
We performed a retrospective observational study, collecting all the reports in EU (EudraVigilance, EV) and US (FAERS) databases of ADRs regarding axicabtagene ciloleucel and tisagenlecleucel. Both descriptive and statistical analyses were performed, the latter by using Reporting Odds Ratio (ROR).

Results
A total number of 1426 reports of suspected ADRs were retrieved in EudraVigilance and FAERS. Patients’ reported age reflected the age range for which the drugs are approved (18–64 years for axicabtagene ciloleucel and patients aged under 25 years for tisagenlecleucel). The most reported event was cytokine release syndrome (CRS), 185 events for tisagenlecleucel and 462 for axicabtagene ciloleucel in FAERS and 137 and 498, respectively, in EudraVigilance. A disproportionality was found comparing axicabtagene ciloleucel with tisagenlecleucel for the above-mentioned event: EV ROR 2.47, 95% CI 2.22–2.74, FAERS 1.89, 1.70–2.10.

Conclusion
CRS represents the major problem with the administration of CAR-T therapies. Our analysis has not revealed new ADRs; however, it supports the safety profile of CAR-T with new data from real clinical setting.
Deep learning for accurately recognizing common causes of shoulder pain on radiographs
Authors: Grauhan Nils F. , Niehues Stefan M. , Gaudin Robert A. , Keller Sarah , Vahldiek Janis L. , Adams Lisa C. , Bressem Keno K. 
Published: February 2021

Abstract
Objective
Training a convolutional neural network (CNN) to detect the most common causes of shoulder pain on plain radiographs and to assess its potential value in serving as an assistive device to physicians.

Materials and methods
We used a CNN of the ResNet-50 architecture which was trained on 2700 shoulder radiographs from clinical practice of multiple institutions. All radiographs were reviewed and labeled for six findings: proximal humeral fractures, joint dislocation, periarticular calcification, osteoarthritis, osteosynthesis, and joint endoprosthesis. The trained model was then evaluated on a separate test dataset, which was previously annotated by three independent expert radiologists. Both the training and the test datasets included radiographs of highly variable image quality to reflect the clinical situation and to foster robustness of the CNN. Performance of the model was evaluated using receiver operating characteristic (ROC) curves, the thereof derived AUC as well as sensitivity and specificity.

Results
The developed CNN demonstrated a high accuracy with an area under the curve (AUC) of 0.871 for detecting fractures, 0.896 for joint dislocation, 0.945 for osteoarthritis, and 0.800 for periarticular calcifications. It also detected osteosynthesis and endoprosthesis with near perfect accuracy (AUC 0.998 and 1.0, respectively). Sensitivity and specificity were 0.75 and 0.86 for fractures, 0.95 and 0.65 for joint dislocation, 0.90 and 0.86 for osteoarthrosis, and 0.60 and 0.89 for calcification.

Conclusion
CNNs have the potential to serve as an assistive device by providing clinicians a means to prioritize worklists or providing additional safety in situations of increased workload.