bluuebunny/crossref_metadata_2025_split huggingface dataset:
StandEnA: a customizable workflow for standardized annotation and generating a presence–absence matrix of proteins
Authors: Chafra Fatma , Borim Correa Felipe , Oni Faith , Konu Karakayalı Özlen , Stadler Peter F , Nunes da Rocha Ulisses 
Published: June 2023

Abstract

Motivation
Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis.

Results
StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence–absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways.

Availability and implementation
StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
JUMP: replicability analysis of high-throughput experiments with applications to spatial transcriptomic studies
Authors: Lyu Pengfei , Li Yan , Wen Xiaoquan , Cao Hongyuan 
Published: June 2023

AbstractMotivationReplicability is the cornerstone of scientific research. The current statistical method for high-dimensional replicability analysis either cannot control the false discovery rate (FDR) or is too conservative.ResultsWe propose a statistical method, JUMP, for the high-dimensional replicability analysis of two studies. The input is a high-dimensional paired sequence of p-values from two studies and the test statistic is the maximum of p-values of the pair. JUMP uses four states of the p-value pairs to indicate whether they are null or non-null. Conditional on the hidden states, JUMP computes the cumulative distribution function of the maximum of p-values for each state to conservatively approximate the probability of rejection under the composite null of replicability. JUMP estimates unknown parameters and uses a step-up procedure to control FDR. By incorporating different states of composite null, JUMP achieves a substantial power gain over existing methods while controlling the FDR. Analyzing two pairs of spatially resolved transcriptomic datasets, JUMP makes biological discoveries that otherwise cannot be obtained by using existing methods.Availability and implementationAn R package JUMP implementing the JUMP method is available on CRAN (https://CRAN.R-project.org/package=JUMP).
Finding motifs using DNA images derived from sparse representations
Authors: Chu Shane K , Stormo Gary D 
Published: June 2023

Abstract

Motivation
Motifs play a crucial role in computational biology, as they provide valuable information about the binding specificity of proteins. However, conventional motif discovery methods typically rely on simple combinatoric or probabilistic approaches, which can be biased by heuristics such as substring-masking for multiple motif discovery. In recent years, deep neural networks have become increasingly popular for motif discovery, as they are capable of capturing complex patterns in data. Nonetheless, inferring motifs from neural networks remains a challenging problem, both from a modeling and computational standpoint, despite the success of these networks in supervised learning tasks.

Results
We present a principled representation learning approach based on a hierarchical sparse representation for motif discovery. Our method effectively discovers gapped, long, or overlapping motifs that we show to commonly exist in next-generation sequencing datasets, in addition to the short and enriched primary binding sites. Our model is fully interpretable, fast, and capable of capturing motifs in a large number of DNA strings. A key concept emerged from our approach—enumerating at the image level—effectively overcomes the k-mers paradigm, enabling modest computational resources for capturing the long and varied but conserved patterns, in addition to capturing the primary binding sites.

Availability and implementation
Our method is available as a Julia package under the MIT license at https://github.com/kchu25/MOTIFs.jl, and the results on experimental data can be found at https://zenodo.org/record/7783033.
Outcomes and Functional Results after Gastropexy without Fundoplication in Patients with Paraoesophageal Hernia
Authors: Teixeira Farinha H , Bomio Pacciorini L , Gaspar Figueiredo S , Demartines N , Mantziari S , Schäfer M 
Published: June 2023

Abstract

Background
Paraoesophageal hernias (PEH) are associated with a high complication rate and often occur in elderly and fragile patients. Gastropexy without fundoplication, in which the stomach is attached to the anterior abdominal wall is an accepted alternative procedure and considered a low-risk intervention. However, outcomes and functional results are hardly described in literature.

Aims
Our study aims to evaluate short-term outcomes and the long-term quality of life of patients that underwent a gastropexy as treatment for PEH.

Methods
Single center cohort analysis of all consecutive patients who underwent hiatal repair and gastropexy for PEH without fundoplication from 2015 to 2021. Postoperative outcomes and functional results were retrospectively collected via chart review of postoperative routine follow-up. Reflux symptoms developed postoperatively were reported using the published and validated quality of life questionnaire: GERD-Health Related Quality of Life Questionnaire (GERD-HRQL). Postoperative complications were reported according to Clavien-Dindo complication grade.

Results
Thirty patients (median age: 72 years (65-80)) were included, 40% classified as ASA III. Main PEH symptoms were reflux (63%), abdominal/thoracic pain (47%), pyrosis (33%), anorexia (30%), and food blockage (26%). Twenty-six laparoscopies were performed (86%). Major complications (III-IVb) occurred in 9 (30%). Seven patients (23%) had PEH recurrence, all re-operated, performing a new gastropexy. Median follow-up was 38 (17-50) months, one patient was lost. Twenty-two patients (75%) reported symptoms resolution with median GERD-HRQL score of 4 (1-6). 72% (n=21) reported operation satisfaction. GERD-HRQL was comparable between patients who were re-operated for recurrence and others: 5 (2-19) versus 3 (0-6), p=0.100.

Conclusions
Gastropexy without fundoplication was performed by laparoscopy in the majority of cases with acceptable complications rates. Two-thirds of patient's report symptoms resolution, and long-term quality-of-live associated to reflux symptoms is good. Although the rate of PEH recurrence requiring a new re-intervention remains increased (23%), it does not seem to affect long-term functional results.
Incidence of Appendix Cancer after Surgery for Colorectal Cancer: Should the Appendix be Prophylactically Removed During Surgery for Colorectal Cancer?
Authors: Meyer J , Wildisen L , Wheeler J , Davies J , Toso C , Meurette G , Ris F 
Published: June 2023

Abstract

Introduction
Retrospective cohort studies with limited sample sizes suggest that the incidence of appendix cancer may be increased in patients having surgery for colorectal cancer.

Aims
To determine whether patients who underwent surgery for colorectal cancer are at higher risk of appendix cancer.

Methods
Cases of colorectal and appendix cancer were identified from the NICER (National Institute for Cancer Epidemiology and Registration, Switzerland) database based on ICD-10 codes for the period 2009-2019. Incidental cases of appendix cancer (all histological types) were extracted from patients who underwent surgery for colorectal cancer and from the general population followed by cantonal cancer registries. Standardized incidence ratios were calculated.

Results
Twenty-eight thousand nine-hundred and thirty-four cases of colorectal cancer and 1,350 cases of appendix cancer were identified over the study period (10 years). After exclusion of cases of appendix cancer, 22,705 patients underwent surgery for colorectal cancer (at-risk population). In these patients, 43 cases of appendix cancer occurred over the follow-up period, including 35 NETs. In the reference population without any history of surgery for colorectal cancer, 1,305 incidental cases of appendix cancer occurred during the same period. This corresponds to an age-standardized incidence of 20.52 per 100,000 person-year in the at-risk population, and of 1.61 per 100,000 person-year in the reference population. The age-standardized incidence ratio for appendix cancer is 12.74 (95% CI: 12.02-13.45) in the at-risk population when compared to the reference population. However, most of these cases were synchronous cancers. To exclude potential information bias, a sensitivity analysis including only cases of left-sided colorectal cancer (colon and rectum) was performed. In this population, the age-standardized incidence ratio for metachronous appendix cancer is 8.67 (95% CI: 7.13-10.20).

Conclusions
The incidence of appendix cancer is increased in patients having surgery for colorectal cancer. The incidence may, however, be too low to consider routine prophylactic appendectomy during surgery for colorectal cancer.
Reconstruction of the Irreparable Proximal Scaphoid with Costo-Osteochondral Graft (Rib Graft)
Authors: Zechmann-Müller N , Heiss-Dunlop W 
Published: June 2023

Abstract

Background
Irreparable proximal pole fractures of the scaphoid remain a real challenge for the treating handsurgeon. Standard salvage options include 4-corner fusion or proximal row carpectomy. These procedures limit the range of motion and have a high rate of conversion to total wrist fusion. The two current biological reconstructive options are the rib graft or the vascularized femoral trochlea osteocartilaginous free flap. In addition, there is the prosthetic semi-replacement arthroplasty using the pyrocarbon adaptive proximal scaphoid implant (APSI).

Aims
To present our series of patients with non-reconstructable proximal scaphoid nonunion/fracture (not suitable for conventional bone graft reconstruction) who were treated by the rib graft technique.

Methods
Our case series of 21 patients treated between March 2013 and January 2019 will been presented (median follow-up 29 months). The surgical technique will be described and crucial technical steps explained. The mean age at surgery was 26 years (SD 5.8) and the median time between injury and rib graft surgery was 2 years (IQR 1.7–3.6). The median postoperative follow-up was 29 months (IQR 19.5–42.4).

Results
All patients returned to their pre-surgical occupation. Significant differences were found in active wrist movements, grip strength, QuickDASH and PRWE pain scores. Union was seen in all 21 patients. The postoperative capitolunate angles were within normal limits. 17/21 patients showed no progessive postoperative osteoarthritic changes, while 4/21 showed slight progression. Progressive ossification of the graft was noted in 14 /21 patients. No donor site complication occurred. One patient failed and underwent excision of the scaphoid and fourcorner fusion 9 months after the rib graft. At the time of revision, the graft was clinically united. We found statistically significant improvements in QuickDASH and PRWE.

Conclusions
Our results suggest that reconstruction of the irreparable proximal pole scaphoid nonunion with costo-osteochondral graft reconstruction (rib graft) is a reliable and straightforward procedure in this challenging problem.
The Contributions of First Nations Voices to the Australian Public Debate over the Criminalisation of Coercive Control
Authors: Hobson Courtney , Salter Michael , Stephenson Jennifer 
Published: June 2023

Abstract
In Australia, there has been significant public debate over the criminalisation of coercive control and the impact on First Nations women and communities. This debate has included allegations of ‘carceral feminists’ using coercive control to advance a punitive agenda that harms First Nations communities. This article drew on the contributions to the public debate on coercive control by First Nations voices to amplify the views of First Nations women and organisations. The findings of the article identified limited and qualified support for criminalisation by First Nations contributors, with the majority of voices opposed to criminalisation, although both First Nations advocates and critics of criminalisation endorsed the need for alternatives to criminalisation. The article concludes that there is significant work to be done by government and non-indigenous organisations to establish criminal justice and child protection systems trusted by First Nations women and communities.
Amyloid-related imaging abnormalities (ARIA): radiological, biological and clinical characteristics
Authors: Hampel Harald , Elhage Aya , Cho Min , Apostolova Liana G , Nicoll James A R , Atri Alireza 
Published: June 2023

AbstractExcess accumulation and aggregation of toxic soluble and insoluble amyloid-β species in the brain are a major hallmark of Alzheimer’s disease. Randomized clinical trials show reduced brain amyloid-β deposits using monoclonal antibodies that target amyloid-β and have identified MRI signal abnormalities called amyloid-related imaging abnormalities (ARIA) as possible spontaneous or treatment-related adverse events. This review provides a comprehensive state-of-the-art conceptual review of radiological features, clinical detection and classification challenges, pathophysiology, underlying biological mechanism(s) and risk factors/predictors associated with ARIA. We summarize the existing literature and current lines of evidence with ARIA-oedema/effusion (ARIA-E) and ARIA-haemosiderosis/microhaemorrhages (ARIA-H) seen across anti-amyloid clinical trials and therapeutic development. Both forms of ARIA may occur, often early, during anti-amyloid-β monoclonal antibody treatment. Across randomized controlled trials, most ARIA cases were asymptomatic. Symptomatic ARIA-E cases often occurred at higher doses and resolved within 3–4 months or upon treatment cessation. Apolipoprotein E haplotype and treatment dosage are major risk factors for ARIA-E and ARIA-H. Presence of any microhaemorrhage on baseline MRI increases the risk of ARIA. ARIA shares many clinical, biological and pathophysiological features with Alzheimer’s disease and cerebral amyloid angiopathy. There is a great need to conceptually link the evident synergistic interplay associated with such underlying conditions to allow clinicians and researchers to further understand, deliberate and investigate on the combined effects of these multiple pathophysiological processes. Moreover, this review article aims to better assist clinicians in detection (either observed via symptoms or visually on MRI), management based on appropriate use recommendations, and general preparedness and awareness when ARIA are observed as well as researchers in the fundamental understanding of the various antibodies in development and their associated risks of ARIA. To facilitate ARIA detection in clinical trials and clinical practice, we recommend the implementation of standardized MRI protocols and rigorous reporting standards. With the availability of approved amyloid-β therapies in the clinic, standardized and rigorous clinical and radiological monitoring and management protocols are required to effectively detect, monitor, and manage ARIA in real-world clinical settings.
Genetic risk scores enhance the diagnostic value of plasma biomarkers of brain amyloidosis
Authors: Ramanan Vijay K , Gebre Robel K , Graff-Radford Jonathan , Hofrenning Ekaterina , Algeciras-Schimnich Alicia , Figdore Daniel J , Lowe Val J , Mielke Michelle M , Knopman David S , Ross Owen A , Jack Clifford R , Petersen Ronald C , Vemuri Prashanthi 
Published: June 2023

Abstract
Blood-based biomarkers offer strong potential to revolutionize diagnosis, trial enrolment and treatment monitoring in Alzheimer’s disease (AD). However, further advances are needed before these biomarkers can achieve wider deployment beyond selective research studies and specialty memory clinics, including the development of frameworks for optimal interpretation of biomarker profiles. We hypothesized that integrating Alzheimer’s disease genetic risk score (AD-GRS) data would enhance the diagnostic value of plasma AD biomarkers by better capturing extant disease heterogeneity. Analysing 962 individuals from a population-based sample, we observed that an AD-GRS was independently associated with amyloid PET levels (an early marker of AD pathophysiology) over and above APOE ε4 or plasma p-tau181, amyloid-β42/40, glial fibrillary acidic protein or neurofilament light chain. Among individuals with a high or moderately high plasma p-tau181, integrating AD-GRS data significantly improved classification accuracy of amyloid PET positivity, including the finding that the combination of a high AD-GRS and high plasma p-tau181 outperformed p-tau181 alone in classifying amyloid PET positivity (88% versus 68%; P = 0.001). A machine learning approach incorporating plasma biomarkers, demographics and the AD-GRS was highly accurate in predicting amyloid PET levels (90% training set; 89% test set) and Shapley value analyses (an explainer method based in cooperative game theory) indicated that the AD-GRS and plasma biomarkers had differential importance in explaining amyloid deposition across individuals. Polygenic risk for AD dementia appears to account for a unique portion of disease heterogeneity, which could non-invasively enhance the interpretation of blood-based AD biomarker profiles in the population.
Intracranial stimulation and EEG feature analysis reveal affective salience network specialization
Authors: Metzger Brian A , Kalva Prathik , Mocchi Madaline M , Cui Brian , Adkinson Joshua A , Wang Zhengjia , Mathura Raissa , Kanja Kourtney , Gavvala Jay , Krishnan Vaishnav , Lin Lu , Maheshwari Atul , Shofty Ben , Magnotti John F , Willie Jon T , Sheth Sameer A , Bijanki Kelly R 
Published: June 2023

Abstract
Emotion is represented in limbic and prefrontal brain areas, herein termed the affective salience network (ASN). Within the ASN, there are substantial unknowns about how valence and emotional intensity are processed—specifically, which nodes are associated with affective bias (a phenomenon in which participants interpret emotions in a manner consistent with their own mood). A recently developed feature detection approach (‘specparam’) was used to select dominant spectral features from human intracranial electrophysiological data, revealing affective specialization within specific nodes of the ASN. Spectral analysis of dominant features at the channel level suggests that dorsal anterior cingulate (dACC), anterior insula and ventral-medial prefrontal cortex (vmPFC) are sensitive to valence and intensity, while the amygdala is primarily sensitive to intensity. Akaike information criterion model comparisons corroborated the spectral analysis findings, suggesting all four nodes are more sensitive to intensity compared to valence. The data also revealed that activity in dACC and vmPFC were predictive of the extent of affective bias in the ratings of facial expressions—a proxy measure of instantaneous mood. To examine causality of the dACC in affective experience, 130 Hz continuous stimulation was applied to dACC while patients viewed and rated emotional faces. Faces were rated significantly happier during stimulation, even after accounting for differences in baseline ratings. Together the data suggest a causal role for dACC during the processing of external affective stimuli.
Interpreting and validating complexity and causality in lesion-symptom prognoses
Authors: Seghier Mohamed L , Price Cathy J 
Published: June 2023

Abstract
This paper considers the steps needed to generate pragmatic and interpretable lesion-symptom mappings that can be used for clinically reliable prognoses. The novel contributions are 3-fold. We first define and inter-relate five neurobiological and five methodological constraints that need to be accounted for when interpreting lesion-symptom associations and generating synthetic lesion data. The first implication is that, because of these constraints, lesion-symptom mapping needs to focus on probabilistic relationships between Lesion and Symptom, with Lesion as a multivariate spatial pattern, Symptom as a time-dependent behavioural profile and evidence that Lesion raises the probability of Symptom. The second implication is that in order to assess the strength of probabilistic causality, we need to distinguish between causal lesion sites, incidental lesion sites, spared but dysfunctional sites and intact sites, all of which might affect the accuracy of the predictions and prognoses generated. We then formulate lesion-symptom mappings in logical notations, including combinatorial rules, that are then used to evaluate and better understand complex brain–behaviour relationships. The logical and theoretical framework presented applies to any type of neurological disorder but is primarily discussed in relationship to stroke damage. Accommodating the identified constraints, we discuss how the 1965 Bradford Hill criteria for inferring probabilistic causality, post hoc, from observed correlations in epidemiology—can be applied to lesion-symptom mapping in stroke survivors. Finally, we propose that rather than rely on post hoc evaluation of how well the causality criteria have been met, the neurobiological and methodological constraints should be addressed, a priori, by changing the experimental design of lesion-symptom mappings and setting up an open platform to share and validate the discovery of reliable and accurate lesion rules that are clinically useful.
Understanding change in traditional sustainable livelihoods: a complex socio-ecological system in an indigenous community in Mexico
Authors: Galán-Guevara Carla 
Published: June 2023

Abstract
This research documents how a transition to a more monetized, trade-based economy modifies the socio-ecological livelihoods system of the indigenous community of Santa Fe de la Laguna, in Mexico. The research found that there had been changes in community livelihoods, from traditional activities (agriculture, forestry, and fishing) to an economy based on handicraft production (pottery) and its trade. Through the modelling of the structure, dynamics, and change processes of the system, two key repercussions are identified: first, pottery production has intensified the extraction of soil and firewood, and second, the increase in trade and the abandonment of traditional activities are diminishing people’s links with nature, which is having an impact on their links with community sociocultural and institutional systems. The paper argues that the most important economic practices and related knowledge of the community may become unviable in the face of livelihood transformations that are responding to the global monetized economy.