bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Reproducibility and Replicability of Deep Learning in Software Engineering
Authors: Liu Chao , Gao Cuiyun , Xia Xin , Lo David , Grundy John , Yang Xiaohu 
Published: October 2021

Context:Deep learning (DL) techniques have gained significant popularity among software engineering (SE) researchers in recent years. This is because they can often solve many SE challenges without enormous manual feature engineering effort and complex domain knowledge.Objective:Although many DL studies have reported substantial advantages over other state-of-the-art models on effectiveness, they often ignore two factors:(1) reproducibility—whether the reported experimental results can be obtained by other researchers using authors’ artifacts (i.e., source code and datasets) with the same experimental setup; and(2) replicability—whether the reported experimental result can be obtained by other researchers using their re-implemented artifacts with a different experimental setup. We observed that DL studies commonly overlook these two factors and declare them as minor threats or leave them for future work. This is mainly due to high model complexity with many manually set parameters and the time-consuming optimization process, unlike classical supervised machine learning (ML) methods (e.g., random forest). This study aims to investigate the urgency and importance of reproducibility and replicability for DL studies on SE tasks.Method:In this study, we conducted a literature review on 147 DL studies recently published in 20 SE venues and 20 AI (Artificial Intelligence) venues to investigate these issues. We also re-ran four representative DL models in SE to investigate important factors that may strongly affect the reproducibility and replicability of a study.Results:Our statistics show the urgency of investigating these two factors in SE, where only 10.2% of the studies investigate any research question to show that their models can address at least one issue of replicability and/or reproducibility. More than 62.6% of the studies do not even share high-quality source code or complete data to support the reproducibility of their complex models. Meanwhile, our experimental results show the importance of reproducibility and replicability, where the reported performance of a DL model could not be reproduced for an unstable optimization process. Replicability could be substantially compromised if the model training is not convergent, or if performance is sensitive to the size of vocabulary and testing data.Conclusion:It is urgent for the SE community to provide a long-lasting link to a high-quality reproduction package, enhance DL-based solution stability and convergence, and avoid performance sensitivity on different sampled data.
Convolutional neural network-based face recognition using non-subsampled shearlet transform and histogram of local feature descriptors
Authors: S Yallamandaiah , Purnachand N. 
Published: October 2021

<span lang="EN-US">Face recognition has been using in a variety of applications like preventing retail crime, unlocking phones, smart advertising, finding missing persons, and protecting law enforcement. However, the ability of face recognition techniques reduces substantially because of changes in pose, illumination, and expressions of the individual. In this paper, a novel face recognition approach based on a non-subsampled shearlet transform (NSST), histogram-based local feature descriptors, and a convolutional neural network (CNN) is proposed. Initially, the Viola-Jones algorithm is used for face detection and then the extracted face region is preprocessed by image resizing operation. Then, NSST decomposes the input image into a low and high-frequency component image. The local feature descriptors such as local phase quantization (LPQ), pyramid of histogram of oriented gradients (PHOG), and the proposed CNN are used for extracting features from the low-frequency component of the NSST decomposition. The extracted features are fused to generate the feature vector and classified using support vector machine (SVM). The efficiency of the suggested method is tested on face databases like Olivetti Research Laboratory (ORL), Yale, and </span><span lang="IN">J</span><span lang="EN-US">apanese female facial expression</span><span lang="IN">(</span><span lang="EN-US">JAFFE</span><span lang="IN">)</span><span lang="EN-US">. The experimental outcomes reveal that the suggested face recognition method outperforms some of the state-of-the-art recognition approaches.</span>
African Witchcraft and Religion among the Yoruba: Translation as Demarcation Practice within a Global Religious History
Authors: Bachmann Judith 
Published: October 2021

Abstract
For years, self-identified witches have demanded the public acknowledgement of witchcraft as “religion” in Nigeria. These political debates are reflected in a long-ongoing scholarly discussion about whether “witchcraft” in Africa should be regarded as religion or not. At its core, this discussion concerns the quest for African meanings. I argue that we should focus on the translingual practice as the reason for today’s perception of “African” and “European” differences as incommensurable. Tracing back today’s understanding of witchcraft among the Yoruba (àjé), the Alatinga anti-witchcraft movement of the early 1950s becomes the nodal point of Yoruba witchcraft history. Discussing the Alatinga as translingual practice, I understand Yoruba witchcraft concepts as products of a global religious history. Only in the aftermath of the Alatinga, a hybrid movement, did the need arise to demarcate “African” and “European” meanings. Thus, Yoruba translingual practice has also affected European understandings of religion and witchcraft today.
Outcomes of Primary Rhegmatogenous Retinal Detachment Repair in Eyes With Preoperative Grade B or C Proliferative Vitreoretinopathy
Authors: Peck Travis J. , Starr Matthew R. , Yonekawa Yoshihiro , Khan M. Ali , Obeid Anthony , Ryan Edwin H. , Ryan Claire , Ammar Michael , Patel Luv G. , Forbes Nora J. , Capone Antonio , Emerson Geoffrey G. , Joseph Daniel P. , Eliott Dean , Regillo Carl D. , Hsu Jason , Gupta Omesh P. , Kuriyan Ajay E. ,   for the Primary Retinal Detachment Outcomes (PRO) Study Group
Published: October 2021

Purpose: This work evaluates the anatomic and functional outcomes of primary rhegmatogenous retinal detachments (RRDs) with preoperative grade B and C proliferative vitreoretinopathy (PVR) vs eyes without PVR. Methods: As a multi-institutional, interventional, retrospective study of all patients undergoing primary RRD surgical procedures from January 1, 2015, through December 31, 2015, this study evaluated the visual acuity (VA) outcomes and single-surgery anatomic success rates (SSAS) of patients with primary grade B and C PVR at the time of RRD repair. Results: A total of 2486 eyes underwent primary RD surgery during the study period, of which 153 eyes (6.2%) had documented preoperative PVR grade B or C. Eyes without PVR had better SSAS compared with eyes with grade B or C PVR (87% vs 83% vs 75%, respectively, P < .0001). Eyes without PVR also had better final mean (SD) logMAR VA (0.35 [0.47]; 20/45 Snellen equivalent) than eyes with PVR of grade B (0.50 [0.56]; 20/63 Snellen equivalent) or grade C ( P < .0001). In only eyes with preoperative PVR, there were no significant differences in final VA or SSAS on multivariate analysis based on surgical approach or use of retinectomy or membrane peeling alone in the intraoperative management of PVR. Conclusions: Eyes with primary preoperative grade B and C PVR appear to have significantly worse VA outcomes and lower surgical success rates. Surgical approach and management of PVR membranes did not appear to affect VA or success rates, indicating that preoperative PVR severity may dictate these outcomes.
Heightened turnover and failed maturation of monocyte-derived macrophages in murine chronic granulomatous disease
Authors: Gibbings Sophie L. , Haist Kelsey C. , Nick Heidi , Frasch S. Courtney , Glass Teagan H. , Vestal Brian , Danhorn Thomas , Mould Kara J. , Henson Peter M. , Bratton Donna L. 
Published: October 2021

AbstractLoss of NADPH oxidase activity leads to altered phagocyte responses and exaggerated inflammation in chronic granulomatous disease (CGD). We sought to assess the effects of Nox2 absence on monocyte-derived macrophages (MoMacs) in gp91phox-/y mice during zymosan-induced peritonitis. MoMacs from CGD and wild-type (WT) peritonea were characterized over time after zymosan injection. Although numbers lavaged from both genotypes were virtually identical, there were marked differences in maturation: newly recruited WT MoMacs rapidly enlarged and matured, losing Ly6C and gaining MHCII, CD206, and CD36, whereas CGD MoMacs remained small and were mostly Ly6C+MHCII–. RNA-sequencing analyses showed few intrinsic differences between genotypes in newly recruited MoMacs but significant differences with time. WT MoMacs displayed changes in metabolism, adhesion, and reparative functions, whereas CGD MoMacs remained inflammatory. PKH dye labeling revealed that although WT MoMacs were mostly recruited within the first 24 hours and remained in the peritoneum while maturing and enlarging, CGD monocytes streamed into the peritoneum for days, with many migrating to the diaphragm where they were found in fibrin(ogen) clots surrounding clusters of neutrophils in nascent pyogranulomata. Importantly, these observations seemed to be driven by milieu: adoptive transfer of CGD MoMacs into inflamed peritonea of WT mice resulted in immunophenotypic maturation and normal behavior, whereas altered maturation/behavior of WT MoMacs resulted from transfer into inflamed peritonea of CGD mice. In addition, Nox2-deficient MoMacs behaved similarly to their Nox2-sufficient counterparts within the largely WT milieu of mixed bone marrow chimeras. These data show persistent recruitment with fundamental failure of MoMac maturation in CGD.
Asxl1 loss cooperates with oncogenic Nras in mice to reprogram the immune microenvironment and drive leukemic transformation
Authors: You Xiaona , Liu Fabao , Binder Moritz , Vedder Alexis , Lasho Terra , Wen Zhi , Gao Xin , Flietner Evan , Rajagopalan Adhithi , Zhou Yun , Finke Christy , Mangaonkar Abhishek , Liao Ruiqi , Kong Guangyao , Ranheim Erik A. , Droin Nathalie , Hunter Anthony M. , Nikolaev Sergey , Balasis Maria , Abdel-Wahab Omar , Levine Ross L. , Will Britta , Nadiminti Kalyan Vara Ganesh , Yang David , Geissler Klaus , Solary Eric , Xu Wei , Padron Eric , Patnaik Mrinal M. , Zhang Jing 
Published: October 2021

Abstract
Mutations in chromatin regulator ASXL1 are frequently identified in myeloid malignancies, in particular ∼40% of patients with chronic myelomonocytic leukemia (CMML). ASXL1 mutations are associated with poor prognosis in CMML and significantly co-occur with NRAS mutations. Here, we show that concurrent ASXL1 and NRAS mutations defined a population of CMML patients who had shorter leukemia-free survival than those with ASXL1 mutation only. Corroborating this human data, Asxl1−/− accelerated CMML progression and promoted CMML transformation to acute myeloid leukemia (AML) in NrasG12D/+ mice. NrasG12D/+;Asxl1−/− (NA) leukemia cells displayed hyperactivation of MEK/ERK signaling, increased global levels of H3K27ac, upregulation of Flt3. Moreover, we find that NA-AML cells overexpressed all the major inhibitory immune checkpoint ligands: programmed death-ligand 1 (PD-L1)/PD-L2, CD155, and CD80/CD86. Among them, overexpression of PD-L1 and CD86 correlated with upregulation of AP-1 transcription factors (TFs) in NA-AML cells. An AP-1 inhibitor or short hairpin RNAs against AP-1 TF Jun decreased PD-L1 and CD86 expression in NA-AML cells. Once NA-AML cells were transplanted into syngeneic recipients, NA-derived T cells were not detectable. Host-derived wild-type T cells overexpressed programmed cell death protein 1 (PD-1) and T-cell immunoreceptor with immunoglobulin and ITIM domains (TIGIT) receptors, leading to a predominant exhausted T-cell phenotype. Combined inhibition of MEK and BET resulted in downregulation of Flt3 and AP-1 expression, partial restoration of the immune microenvironment, enhancement of CD8 T-cell cytotoxicity, and prolonged survival in NA-AML mice. Our study suggests that combined targeted therapy and immunotherapy may be beneficial for treating secondary AML with concurrent ASXL1 and NRAS mutations.
Why is AAV FVIII gene therapy not approved by the US Food and Drug Administration yet?
Authors: Arruda Valder R. 
Published: October 2021

Abstract
The prospect of a clinical strategy using an adeno-associated virus (AAV) vector for expression of therapeutic levels of factor VIII (FVIII) has been highly desirable. This was initially anticipated by promising data from clinical studies on AAV5-FVIII in men with severe hemophilia A. However, long-term follow-up showed a unique efficacy concern on the sustainability and durability derived from a continuous decline in the FVIII transgene levels starting 1 year after vector injection through year 5. Additional follow-up of early-phase studies and outcomes of an ongoing phase 3 study will likely provide evidence on the feasibility of this approach. Here, the potential underlying mechanisms of the FVIII declining levels, together with the revision of several unique early and late onset findings, are discussed. The lack of long-term preclinical studies in large animal models prevents the firm conclusion that FVIII levels decline was unexpected. It is possible that the combination of vector manufacturing platform and dose, accompanied with ectopic expression of supraphysiologic levels of FVIII at short-term follow-up, may all contribute to the sustainability and durability of the transgene levels. Notably, vector readministration to further improve the FVIII levels is not feasible at this time. Thus, the need of a one-and-done AAV strategy to achieve sustain FVIII levels of expression is sine qua non to impact favorably the disease phenotype.
Primary graft failure, but not relapse, may be identified by early chimerism following double cord blood unit transplantation
Authors: Hough Rachael , Lopes Andre , Patrick Pip , Russell Nigel , Raj Kavita , Tholouli Eleni , A. Snowden John , Collin Matthew , El-Mehidi Nadjet , Lawrie Anthony , Clifton-Hadley Laura , Veys Paul , Craddock Charles , Mackinnon Stephen , Cook Gordon , Shaw Bronwen , Marks David 
Published: October 2021

Abstract
Umbilical cord blood transplantation (UCBT) has increased access to potentially curative therapy for patients with life-threatening disorders of the bone marrow and immune system. The introduction of reduced intensity conditioning (RIC) regimens and double umbilical cord unit infusions (DUCBT) has broadened the applicability of UCBT to more frail or larger recipients. The kinetics of chimerism after RIC DUCBT and their clinical utility are poorly understood. The RIC CBT trial reported here sought to prospectively evaluate the role of lineage-specific chimerism after DUCBT in adult patients with hematologic malignancies in the United Kingdom. Fifty-eight patients with a median age of 52 years were recruited, with overall and progression-free survivals of 59% (95% confidence interval [CI], 45%-71%) and 52% (95% CI, 39%-64%), respectively, at 2 years. Nonrelapse mortality was 4% (95% CI, 1%-13%) at day 100, and the relapse rate was 31% (95% CI, 21%-45%) at 1 year. Peripheral blood lineage-specific chimerism was feasible from day 7 after transplant onward. Five patterns of chimerism were observed including (1) complete single unit dominance (39 patients), (2) sustained donor-donor mixed chimerism (3 patients), (3) sustained donor-recipient mixed chimerism (5 patients), (4) dominance reversion (1 patient), and (5) primary graft failure (4 patients). The RIC CBT trial enabled adult patients with high-risk hematologic malignancies to safely access UCBT in the United Kingdom and provided novel insights into the kinetics of donor and recipient chimerism after RIC DUCBT that are clinically relevant. This trial was registered at https://www.clinicaltrialsregister.eu/ctr-search/trial/2004-003845-41/GB as #NCT00959231 and EudraCT 2004-003845-41.
Genome-wide analysis of Claviceps paspali: insights into the secretome of the main species causing ergot disease in Paspalum spp
Authors: Oberti H. , Spangenberg G. , Cogan N. , Reyno R. , Feijoo M. , Murchio S. , Dalla-Rizza M. 
Published: October 2021

Abstract
Background
The phytopatogen Claviceps paspali is the causal agent of Ergot disease in Paspalum spp., which includes highly productive forage grasses such as P. dilatatum. This disease impacts dairy and beef production by affecting seed quality and producing mycotoxins that can affect performance in feeding animals. The molecular basis of pathogenicity of C. paspali remains unknown, which makes it more difficult to find solutions for this problem. Secreted proteins are related to fungi virulence and can manipulate plant immunity acting on different subcellular localizations. Therefore, identifying and characterizing secreted proteins in phytopathogenic fungi will provide a better understanding of how they overcome host defense and cause disease. The aim of this work is to analyze the whole genome sequences of three C. paspali isolates to obtain a comparative genome characterization based on possible secreted proteins and pathogenicity factors present in their genome. In planta RNA-seq analysis at an early stage of the interaction of C. paspali with P. dilatatum stigmas was also conducted in order to determine possible secreted proteins expressed in the infection process.

Results
C. paspali isolates had compact genomes and secretome which accounted for 4.6–4.9% of the predicted proteomes. More than 50% of the predicted secretome had no homology to known proteins. RNA-Seq revealed that three protein-coding genes predicted as secreted have mayor expression changes during 1 dpi vs 4 dpi. Also, three of the first 10 highly expressed genes in both time points were predicted as effector-like. CAZyme-like proteins were found in the predicted secretome and the most abundant family could be associated to pectine degradation. Based on this, pectine could be a main component affected by the cell wall degrading enzymes of C. paspali.

Conclusions
Based on predictions from DNA sequence and RNA-seq, unique probable secreted proteins and probable pathogenicity factors were identified in C. paspali isolates. This information opens new avenues in the study of the biology of this fungus and how it modulates the interaction with its host. Knowledge of the diversity of the secretome and putative pathogenicity genes should facilitate future research in disease management of Claviceps spp.
Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals
Authors: Chai Simin , Huang Xin , Wu Tianzhen , Xu Shixia , Ren Wenhua , Yang Guang 
Published: October 2021

Abstract
Background
Mammals have wide variations in testicular position, with scrotal testes in some species and ascrotal testes in others. Although cryptorchidism is hazardous to human health, some mammalian taxa are natural cryptorchids. However, the evolution of testicular position and the molecular mechanisms underlying the maintenance of health, including reproductive health, in ascrotal mammals are not clear.

Results
In the present study, comparative genomics and evolutionary analyses revealed that genes associated with the extracellular matrix and muscle, contributing to the development of the gubernaculum, were involved in the evolution of testicular position in mammals. Moreover, genes related to testicular position were significantly associated with spermatogenesis and sperm fertility. These genes showed rapid evolution and the signature of positive selection, with specific substitutions in ascrotal mammals. Genes associated with testicular position were significantly enriched in functions and pathways related to cancer, DNA repair, DNA replication, and autophagy.

Conclusions
Our results revealed that alterations in gubernaculum development contributed to the evolution of testicular position in mammals and provided the first support for two hypotheses for variation in testicular position in mammals, the “cooling hypothesis”, which proposes that the scrotum provides a cool environment for acutely heat-sensitive sperm and the “training hypothesis”, which proposes that the scrotum develops the sperm by exposing them to an exterior environment. Further, we identified cancer resistance and DNA repair as potential protective mechanisms in natural cryptorchids. These findings provide general insights into cryptorchidism and have implications for health and infertility both in humans and domestic mammals.
A rare variation of duplicated portal vein: left branch derived from splenic vein mimicking cavernous transformation
Authors: Yang Qian , Li Jun , Wang Hanwei , Wang Shunan 
Published: October 2021

Abstract
Background
Duplication of the portal vein is a rare type of anatomic variant of the portal vein (PV) system that can be incidentally found and can lead to various challenges and consequences. Herein, we report an unusual case to increase our understanding of such anatomic variants.

Case presentation
A 67-year-old asymptomatic woman was diagnosed with a liver space-occupying lesion by ultrasonography on a routine physical examination. The laboratory examinations from a local hospital suggested that her liver function tests were normal. The liver appeared normal on pre-contrast enhanced CT images. However, there were multiple complex abnormalities of PV found on contrast-enhanced CT scans, including two independent sources of PV (duplication), preduodenal PV, circum-portal pancreas, mimic cavernous transformation, abnormal branches of PV, and transient abnormal perfusion in the left lobe of the liver. MRI showed fatty infiltration in the left lobe of the liver.

Conclusion
This case extends our current understanding of the anatomical variations of the PV system. Knowledge of these complex and rare anatomical variations will help clinical doctors make a confident diagnosis or assist with proper planning of a surgical procedure.