bluuebunny/crossref_metadata_2025_split huggingface dataset:
LaMiNa: A Creative Synergistic Approach to Facial Rejuvenation
Authors: Claytor Richard Brannon , Sheck Casey , Jones India , Quigley Robert 
Published: March 2023

Abstract

Background
Treating facial aging with CO2 lasering or microneedling are cornerstones of facial rejuvenation. Skin rejuvenation utilizing thermal and mechanical treatments have historically been considered too injurious to be combined at a single setting. Autologous nanofat has been shown to deliver wound healing properties. We investigated the safety and efficacy of co-terminus CO2 lasering and microneedling to resolve fine lines and rhytids in facial skin with addition of autologous nanofat to aid in recovery.

Objectives
Combination treatments may result in better results with faster recovery. We investigated the safety and efficacy of co-terminus CO2 lasering and microneedling to resolve fine lines and rhytids in facial skin with addition of autologous nanofat to aid in recovery.

Methods
Twenty-three patients underwent facial treatment with CO2 lasering followed by microneedling and application of autologous nanofat (LaMiNa). One volunteer patient had tissue biopsies of treatment areas to demonstrate histologic tissue level changes.

Results
All patients verbally reported no pain (Numerical Rating System 0–10) following procedure and had rapid recovery within an average of 5 days. Pathology results demonstrated that CO2 and microneedling had persistent epidermal disruption and perineural inflammation at 4 days, while the introduction of autologous nanofat at the time of CO2 and microneedling resulted in full recovery of epidermis and resolution of perineural inflammation.

Conclusions
Triple therapy (LaMiNa) with thermal CO2 remodeling and mechanical microneedling penetration have accelerated and pain-free recovery with the addition of autologous nanofat. Histologic analysis reveals that epidermal recovery is accelerated and perineural inflammation is reduced with the addition of autologous nanofat following skin remodeling from combined CO2 and microneedling.

Level of Evidence: 3
TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning
Authors: Wang Guangshuai , Wu Tao , Ning Wei , Diao Kaixuan , Sun Xiaoqin , Wang Jinyu , Wu Chenxu , Chen Jing , Xu Dongliang , Liu Xue-Song 
Published: March 2023

Abstract
Major histocompatibility complex (MHC) class II molecules play a pivotal role in antigen presentation and CD4+ T cell response. Accurate prediction of the immunogenicity of MHC class II-associated antigens is critical for vaccine design and cancer immunotherapies. However, current computational methods are limited by insufficient training data and algorithmic constraints, and the rules that govern which peptides are truly recognized by existing T cell receptors remain poorly understood. Here, we build a transfer learning-based, long short-term memory model named ‘TLimmuno2’ to predict whether epitope-MHC class II complex can elicit T cell response. Through leveraging binding affinity data, TLimmuno2 shows superior performance compared with existing models on independent validation datasets. TLimmuno2 can find real immunogenic neoantigen in real-world cancer immunotherapy data. The identification of significant MHC class II neoantigen-mediated immunoediting signal in the cancer genome atlas pan-cancer dataset further suggests the robustness of TLimmuno2 in identifying really immunogenic neoantigens that are undergoing negative selection during cancer evolution. Overall, TLimmuno2 is a powerful tool for the immunogenicity prediction of MHC class II presented epitopes and could promote the development of personalized immunotherapies.
Peak Pair Pruner: a post-processing software to MS-DIAL for peak pair validation and ratio quantification of isotopic labeling LC-MS(/MS) data
Authors: Smith Ryan A , Zhang Qibin 
Published: March 2023

AbstractMotivationIsotopic labeling is an essential relative quantification strategy in mass spectrometry-based metabolomics, ideal for studying large cohorts by minimizing common sources of variations in quantitation. MS-DIAL is a free and popular general metabolomics platform that has isotopic labeling data processing capabilities but lacks features provided by other software specialized for isotopic labeling data analysis, such as isotopic pair validation and tabular light-to-heavy peak ratio reporting.ResultsWe developed Peak Pair Pruner (PPP), a standalone Python program for post-processing of MS-DIAL alignment matrixes. PPP provides these missing features and innovation including isotopic overlap subtraction based on a light-tagged pool sample as quality control. The MS-DIAL+PPP workflow for isotopic labeling-based metabolomics data processing was validated using light and heavy dansylated amino acid standard mixture and metabolite extract from human plasma.Availability and implementationPeak Pair Pruner is freely available on Github: https://github.com/QibinZhangLab/Peak_Pair_Pruner. Raw MS data and .ibf files analyzed are on Metabolomics Workbench with Study ID ST002427.Contactq_zhang2@uncg.eduSupplementary informationSupplementary data are available at Bioinformatics Advances online.
A framework for high-throughput sequence alignment using real processing-in-memory systems
Authors: Diab Safaa , Nassereldine Amir , Alser Mohammed , Gómez Luna Juan , Mutlu Onur , El Hajj Izzat 
Published: March 2023

Abstract

Motivation
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory (PIM) architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using PIM, and evaluate it on UPMEM, the first publicly available general-purpose programmable PIM system.

Results
Our evaluation shows that a real PIM system can substantially outperform server-grade multi-threaded CPU systems running at full-scale when performing sequence alignment for a variety of algorithms, read lengths, and edit distance thresholds. We hope that our findings inspire more work on creating and accelerating bioinformatics algorithms for such real PIM systems.

Availability and implementation
Our code is available at https://github.com/safaad/aim.
Impact of complications after resection of pancreatic cancer on disease recurrence and survival, and mediation effect of adjuvant chemotherapy: nationwide, observational cohort study
Authors: Henry Anne Claire , van Dongen Jelle C , van Goor Iris W J M , Smits F Jasmijn , Nagelhout Anne , Besselink Marc G , Busch Olivier R , Bonsing Bert A , Bosscha Koop , van Dam Ronald M , Festen Sebastiaan , Groot Koerkamp Bas , van der Harst Erwin , de Hingh Ignace H , van der Kolk Marion , Liem Mike S L , de Meijer Vincent E , Patijn Gijs A , Roos Daphne , Schreinemakers Jennifer M , Wit Fennie , Daamen Lois A , van Santvoort Hjalmar C , Molenaar I Quintus , van Eijck Casper H J 
Published: March 2023

Abstract

Background
The causal pathway between complications after pancreatic cancer resection and impaired long-term survival remains unknown. The aim of this study was to investigate the impact of complications after pancreatic cancer resection on disease-free interval and overall survival, with adjuvant chemotherapy as a mediator.

Methods
This observational study included all patients undergoing pancreatic cancer resection in the Netherlands (2014–2017). Clinical data were extracted from the prospective Dutch Pancreatic Cancer Audit. Recurrence and survival data were collected additionally. In causal mediation analysis, direct and indirect effect estimates via adjuvant chemotherapy were calculated.

Results
In total, 1071 patients were included. Major complications (hazards ratio 1.22 (95 per cent c.i. 1.04 to 1.43); P = 0.015 and hazards ratio 1.25 (95 per cent c.i. 1.08 to 1.46); P = 0.003) and organ failure (hazards ratio 1.86 (95 per cent c.i. 1.32 to 2.62); P &lt; 0.001 and hazards ratio 1.89 (95 per cent c.i. 1.36 to 2.63); P &lt; 0.001) were associated with shorter disease-free interval and overall survival respectively. The effects of major complications and organ failure on disease-free interval (−1.71 (95 per cent c.i. −2.27 to −1.05) and −3.05 (95 per cent c.i. −4.03 to −1.80) respectively) and overall survival (−1.92 (95 per cent c.i. −2.60 to −1.16) and −3.49 (95 per cent c.i. −4.84 to −2.03) respectively) were mediated by adjuvant chemotherapy. Additionally, organ failure directly affected disease-free interval (−5.38 (95 per cent c.i. −9.27 to −1.94)) and overall survival (−6.32 (95 per cent c.i. −10.43 to −1.99)). In subgroup analyses, the association was found in patients undergoing pancreaticoduodenectomy, but not in patients undergoing distal pancreatectomy.

Conclusion
Major complications, including organ failure, negatively impact survival in patients after pancreatic cancer resection, largely mediated by adjuvant chemotherapy. Prevention or adequate treatment of complications and use of neoadjuvant treatment may improve oncological outcomes.
Comparing the brain–behaviour relationship in acute and chronic stroke aphasia
Authors: Busby Natalie , Hillis Argye E , Bunker Lisa , Rorden Chis , Newman-Norlund Roger , Bonilha Leo , Meier Erin , Goldberg Emily , Hickok Gregory , Yourganov Grigori , Fridriksson Julius 
Published: March 2023

AbstractIn stroke aphasia, lesion volume is typically associated with aphasia severity. Although this relationship is likely present throughout recovery, different factors may affect lesion volume and behaviour early into recovery (acute) and in the later stages of recovery (chronic). Therefore, studies typically separate patients into two groups (acute/chronic), and this is often accompanied with arguments for and against using data from acute stroke patients over chronic. However, no comprehensive studies have provided strong evidence of whether the lesion–behaviour relationship early in recovery is comparable to later in the recovery trajectory. To that end, we investigated two aims: (i) whether lesion data from acute and chronic patients yield similar results in region-based lesion-symptom mapping analyses and (ii) if models based on one timepoint accurately predict the other. Lesions and aphasia severity scores from acute (N = 63) and chronic (N = 109) stroke survivors with aphasia were entered into separate univariate region-based lesion-symptom mapping analyses. A support vector regression model was trained on lesion data from either the acute or chronic data set to give an estimate of aphasia severity. Four model-based analyses were conducted: trained on acute/chronic using leave-one-out, tested on left-out behaviour or trained on acute/chronic to predict the other timepoint. Region-based lesion-symptom mapping analyses identified similar but not identical regions in both timepoints. All four models revealed positive correlations between actual and predicted Western Aphasia Battery-Revised aphasia-quotient scores. Lesion-to-behaviour predictions were almost equivalent when comparing within versus across stroke stage, despite differing lesion size/locations and distributions of aphasia severity between stroke timepoints. This suggests that research investigating the brain–behaviour relationship including subsets of patients from only one timepoint may also be applicable at other timepoints, although it is important to note that these comparable findings may only be seen using broad measures such as aphasia severity, rather than those aimed at identifying more specific deficits. Subtle differences found between timepoints may also be useful in understanding the nature of lesion volume and aphasia severity over time. Stronger correlations found when predicting acute behaviour (e.g. predicting acute: r = 0.6888, P &lt; 0.001, predicting chronic r = 0.5014, P &lt; 0.001) suggest that the acute lesion/perfusion patterns more accurately capture the critical changes in underlying vascular territories. Differences in critical brain regions between timepoints may shed light on recovery patterns. Future studies could focus on a longitudinal design to compare acute and chronic patients in a more controlled manner.
Multiomics-empowered Deep Phenotyping of Ulcerative Colitis Identifies Biomarker Signatures Reporting Functional Remission States
Authors: Janker Lukas , Schuster Dina , Bortel Patricia , Hagn Gerhard , Meier-Menches Samuel M , Mohr Thomas , Mader Johanna C , Slany Astrid , Bileck Andrea , Brunmair Julia , Madl Christian , Unger Lukas , Hennlich Barbara , Weitmayr Barbara , Del Favero Giorgia , Pils Dietmar , Pukrop Tobias , Pfisterer Nikolaus , Feichtenschlager Thomas , Gerner Christopher 
Published: March 2023

Abstract

Introduction
Ulcerative colitis [UC] is a chronic disease with rising incidence and unclear aetiology. Deep molecular phenotyping by multiomics analyses may provide novel insights into disease processes and characteristic features of remission states.

Methods
UC pathomechanisms were assessed by proteome profiling of human tissue specimens, obtained from five distinct colon locations for each of the 12 patients included in the study. Systemic disease-associated alterations were evaluated thanks to a cross-sectional setting of mass spectrometry-based multiomics analyses comprising proteins, metabolites, and eicosanoids of plasma obtained from UC patients during acute episodes and upon remission, in comparison with healthy controls.

Results
Tissue proteome profiling indicated colitis-associated activation of neutrophils, macrophages, B and T cells, fibroblasts, endothelial cells and platelets, and hypoxic stress, and suggested a general downregulation of mitochondrial proteins accompanying the establishment of apparent wound healing-promoting activities including scar formation. Whereas pro-inflammatory proteins were apparently upregulated by immune cells, the colitis-associated epithelial cells, fibroblasts, endothelial cells, and platelets seemed to predominantly contribute anti-inflammatory and wound healing-promoting proteins. Blood plasma proteomics indicated chronic inflammation and platelet activation, whereas plasma metabolomics identified disease-associated deregulations of gut and gut microbiome-derived metabolites. Upon remission several, but not all, molecular candidate biomarker levels recovered back to normal.

Conclusion
The findings may indicate that microvascular damage and platelet deregulation hardly resolve upon remission, but apparently persist as disease-associated molecular signatures. This study presents local and systemic molecular alterations integrated in a model for UC pathomechanisms, potentially supporting the assessment of disease and remission states in UC patients.
Epicardial connection(s) inside the pulmonary vein antrum isolation lines contribute to subsequent atrial fibrillation: a case report
Authors: Fujiwara Masaki , Takemoto Masao , Koga Tokushi , Tsuchihashi Takuya 
Published: March 2023

Abstract

Aims
Recent reports have demonstrated that ∼10% of patients with atrial fibrillation (AF) have epicardial connections (ECs) inside the pulmonary vein (PV) antrum isolation (AI) (PVAI) lines, which could be a possible mechanism of failure to achieve a complete PVAI, thus contributing to AF recurrence.

Case summary
We present an 80-year-old female case with consistently continuing AF associated with ECs. Epicardial connections involving the PVs were detected in the left and right superior PVs after the completion of the PVAI. The AF steadily terminated after the ablation of those ECs. She has remained well without any AF or symptoms for 2 years post-ablation.

Discussion
Those ECs might have played a possible important role in initiating and maintaining the AF. The mechanism(s) of the ECs may be a cornerstone of the failure to achieve a complete PVAI contributing to AF recurrence. Ablation of the EC(s) in addition to the PVAI may be better able to achieve the completion of the PVAI. Thus, physicians should be aware of the possibility of the presence of EC(s) when performing ablation of AF, even though complete PVAI lines have been achieved.
Effect of genetic variants in UBE2O and TPK1 on facial morphology of Koreans
Authors: Cho Hye-Won , Ban Hyo-Jeong , Jin Hyun-Seok , Cha Seongwon , Eom Yong-Bin 
Published: March 2023

Abstract

Human face is a highly heritable and complex trait. Many genome-wide analyses have identified genetic variants influencing facial morphology. Genome-wide association studies (GWASs) investigating facial morphologies of different populations provide a comprehensive insight into the genetic basis of the human face. Here, we report a GWAS of normal facial variation in Koreans using an array optimized for the Korean population (KoreanChip). We found that novel genetic variants encompassing four loci reached the genome-wide significance threshold. They include LOC107984547, UBE2O, TPK1, and LINC01148 loci associated with facial angle, brow ridge protrusion, nasal height, and eyelid curvature. Our results also validated previously published genetic loci, including FAT4, SOX9, and TBX3 loci. All confirmed genetic variants showed phenotypic differences involving each facial trait based on the effect of the minor allele. The present study highlights genetic signals associated with normal human facial variation and provides candidates for functional studies.

Key points
Magma transport along structural boundaries in the upper crust: insights from broad-band magnetotelluric constraints on the structure beneath Unzen volcano, Japan
Authors: Triahadini Agnis , Aizawa Koki , Hashimoto Tasuku M , Chiba Keita , Uchida Kazunari , Yamamoto Yuto , Miyano Kanta , Muramatsu Dan , Aniya Satoru , Okubo Ayumu , Kawamura Yuta 
Published: March 2023

SUMMARYUnzen volcano, located on Shimabara Peninsula, Nagasaki, Japan, is an active volcano that has been intensively monitored since 1989, one year before the most recent eruption in 1990–1995. Previous earthquake and surface deformation studies have revealed that magma is transported obliquely from a magma reservoir beneath Tachibana Bay, to the west of Shimabara Peninsula. Here, we conduct broad-band magnetotelluric (MT) surveys at 99 sites around Shimabara Peninsula to investigate the crustal structure beneath Unzen volcano that is related to magma migration. A 3-D resistivity model that is constructed from 25 broad-band MT sites and 45 telluric sites shows a broad high-resistivity zone beneath Shimabara Peninsula and low-resistivity zones to the west and east of the peninsula. An unexpected observation is the spatial alignment of the high-resistivity zone with a seismic low-velocity zone (LVZ) at 3–15 km depth. Quantitative analysis indicates this high-resistivity zone contains &lt; 0.7 per cent melt under the assumption that the melt is stored in a good porosity network, while &lt; 11 per cent melt in relatively poor pore network. We infer this high-resistivity, LVZ to be a highly crystallized mush zone (HCMZ) with low permeability. The hypocentres and pressure sources of the 1990–1995 eruption are distributed along the boundary between the high- and low-resistivity zones beneath the western part of the peninsula. We therefore conclude that the magma migrated along a structural boundary that possessed a relatively high permeability. Previous studies have suggested that eruptible magma is usually transported vertically upward through the centre of the mush zone, whereas the present results reveal that magma can be transported along the upper boundary of an HCMZ.
I think that I will just sit here and wait
Authors: Beamish Richard 
Published: March 2023

Abstract
Fisheries research has always been an opportunity of discovery for me and never really a job. Finding a new species of fish, discovering that fish can outlive humans, or that atmospheric transport of chemicals can profoundly affect fish survival over vast distances kept each day exciting. So many people I worked with or met remain as wonderful memories. There are now much better opportunities for discoveries of mechanisms responsible for the dynamics of fish populations than in the past. There is also an urgency for these discoveries as our changing climate affects the capacity of habitats to support fish. We need young people in spirit who can work in teams that excel in pursuing these new opportunities.
You’re Not the Boss of me, Algorithm: Increased User Control and Positive Implicit Attitudes Are Related to Greater Adherence to an Algorithmic Aid
Authors: Morrison Ben W , Kelson Joshua N , Morrison Natalie M V , Innes J Michael , Zelic Gregory , Al-Saggaf Yeslam , Paul Manoranjan 
Published: March 2023

Abstract
This study examined whether participants’ adherence to an algorithmic aid was related to the degree of control they were provided at decision point and their attitudes toward new technologies and algorithms. It also tested the influence of control on participants’ subjective reports of task demands whilst using the aid. A total of 159 participants completed an online experiment centred on a simulated forecasting task, which required participants to predict the performance of school students on a standardized mathematics test. For each student, participants also received an algorithm-generated forecast of their score. Participants were randomly assigned to either the ‘full control’ (adjust forecast as much as they wish), ‘moderate control’ (adjust forecast by 30%) or ‘restricted control’ (adjust forecast by 2%) group. Participants then completed an assessment of subjective task load, a measure of their explicit attitudes toward new technologies, demographic and experience items (age, gender and computer literacy) and a novel version of the Go/No-Go Association Task, which tested their implicit attitudes toward algorithms. The results revealed that participants who were provided with more control over the final forecast tended to deviate from it more greatly and reported lower levels of frustration. Furthermore, participants showing more positive implicit attitudes toward algorithms were found to deviate less from the algorithm’s forecasts, irrespective of the degree of control they were given. The findings allude to the importance of users’ control and preexisting attitudes in their acceptance of, and frustration in using a novel algorithmic aid, which may ultimately contribute to their intention to use them in the workplace. These findings can guide system developers and support workplaces implementing expert system technology.
Measuring Galactic dark matter through unsupervised machine learning
Authors: Buckley Matthew R , Lim Sung Hak , Putney Eric , Shih David 
Published: March 2023

ABSTRACT
Measuring the density profile of dark matter in the Solar neighbourhood has important implications for both dark matter theory and experiment. In this work, we apply autoregressive flows to stars from a realistic simulation of a Milky Way-type galaxy to learn – in an unsupervised way – the stellar phase space density and its derivatives. With these as inputs, and under the assumption of dynamic equilibrium, the gravitational acceleration field and mass density can be calculated directly from the Boltzmann equation without the need to assume either cylindrical symmetry or specific functional forms for the galaxy’s mass density. We demonstrate our approach can accurately reconstruct the mass density and acceleration profiles of the simulated galaxy, even in the presence of Gaia-like errors in the kinematic measurements.