bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequential autoencoders for feature engineering and pretraining in major depressive disorder risk prediction
Authors: Jones Barrett W , Taylor Warren D , Walsh Colin G 
Published: October 2023

Abstract

Objectives
We evaluated autoencoders as a feature engineering and pretraining technique to improve major depressive disorder (MDD) prognostic risk prediction. Autoencoders can represent temporal feature relationships not identified by aggregate features. The predictive performance of autoencoders of multiple sequential structures was evaluated as feature engineering and pretraining strategies on an array of prediction tasks and compared to a restricted Boltzmann machine (RBM) and random forests as a benchmark.

Materials and Methods
We study MDD patients from Vanderbilt University Medical Center. Autoencoder models with Attention and long-short-term memory (LSTM) layers were trained to create latent representations of the input data. Predictive performance was evaluated temporally by fitting random forest models to predict future outcomes with engineered features as input and using autoencoder weights to initialize neural network layers. We evaluated area under the precision-recall curve (AUPRC) trends and variation over the study population’s treatment course.

Results
The pretrained LSTM model improved predictive performance over pretrained Attention models and benchmarks in 3 of 4 outcomes including self-harm/suicide attempt (AUPRCs, LSTM pretrained = 0.012, Attention pretrained = 0.010, RBM = 0.009, random forest = 0.005). The use of autoencoders for feature engineering had varied results, with benchmarks outperforming LSTM and Attention encodings on the self-harm/suicide attempt outcome (AUPRCs, LSTM encodings = 0.003, Attention encodings = 0.004, RBM = 0.009, random forest = 0.005).

Discussion
Improvement in prediction resulting from pretraining has the potential for increased clinical impact of MDD risk models. We did not find evidence that the use of temporal feature encodings was additive to predictive performance in the study population. This suggests that predictive information retained by model weights may be lost during encoding. LSTM pretrained model predictive performance is shown to be clinically useful and improves over state-of-the-art predictors in the MDD phenotype. LSTM model performance warrants consideration of use in future related studies.

Conclusion
LSTM models with pretrained weights from autoencoders were able to outperform the benchmark and a pretrained Attention model. Future researchers developing risk models in MDD may benefit from the use of LSTM autoencoder pretrained weights.
Capital shocks and the great urban divide
Authors: Daams Michiel N , McCann Philip , Veneri Paolo , Barkham Richard , Schoenmaker Dennis 
Published: October 2023

Abstract
This article exploits signals of capital pricing and availability in US cities which are obtained from uniquely detailed data on real estate investments. We identify how places were differently affected by the global financial crisis and provide insights which offer an alternative explanation of why US economic growth continues to experience spatial divergence after many decades of convergence. Investment pricing uncovers that before the crisis capital was allocated efficiently across localities, whereas the global financial shock favored large and prosperous places. These findings point to persistent post-crisis asymmetry in local capital market conditions and underscore the capital risk-safety aspects of agglomeration.
Polyamines mediate the inhibitory effect of drought stress on nitrogen reallocation and utilization to regulate grain number in wheat
Authors: Li Juan , Li Qi , Guo Nian , Xian Qinglin , Lan Bing , Nangia Vinay , Mo Fei , Liu Yang 
Published: October 2023

Abstract
Drought stress poses a serious threat to grain formation in wheat. Nitrogen (N) plays crucial roles in plant organ development; however, the physiological mechanisms by which drought stress affects plant N availability and mediates the formation of grains in spikes of winter wheat are still unclear. In this study, we determined that pre-reproductive drought stress significantly reduced the number of fertile florets and the number of grains formed. Transcriptome analysis demonstrated that this was related to N metabolism, and in particular, the metabolism pathways of arginine (the main precursor for synthesis of polyamine) and proline. Continuous drought stress restricted plant N accumulation and reallocation rates, and plants preferentially allocated more N to spike development. As the activities of amino acid biosynthesis enzymes and catabolic enzymes were inhibited, more free amino acids accumulated in young spikes. The expression of polyamine synthase genes was down-regulated under drought stress, whilst expression of genes encoding catabolic enzymes was enhanced, resulting in reductions in endogenous spermidine and putrescine. Treatment with exogenous spermidine optimized N allocation in young spikes and leaves, which greatly alleviated the drought-induced reduction in the number of grains per spike. Overall, our results show that pre-reproductive drought stress affects wheat grain numbers by regulating N redistribution and polyamine metabolism.
NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes
Authors: Baltoumas Fotis A , Karatzas Evangelos , Liu Sirui , Ovchinnikov Sergey , Sofianatos Yorgos , Chen I-Min , Kyrpides Nikos C , Pavlopoulos Georgios A 
Published: October 2023

Abstract
The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins of reference genomes or Pfam domains. Each protein family is accompanied by multiple sequence alignments, Hidden Markov Models, taxonomic information, ecosystem and geolocation metadata, sequence and structure predictions, as well as 3D structure models predicted with AlphaFold2. In its current version, NMPFamsDB hosts over 100 000 protein families, each with at least 100 members. The reported protein families significantly expand (more than double) the number of known protein sequence clusters from reference genomes and reveal new insights into their habitat distribution, origins, functions and taxonomy. We expect NMPFamsDB to be a valuable resource for microbial proteome-wide analyses and for further discovery and characterization of novel functions. NMPFamsDB is publicly available in http://www.nmpfamsdb.org/ or https://bib.fleming.gr/NMPFamsDB.
A biomimetic chip to assess subcutaneous bioavailability of monoclonal antibodies in humans
Authors: Chandran Suja Vineeth , Qi Qin M , Halloran Kevin , Zhang Jifeng , Shaha Suyog , Prakash Supriya , Kumbhojkar Ninad , Deslandes Antoine , Huille Sylvain , Gokarn Yatin R , Mitragotri Samir 
Published: October 2023

Abstract
Subcutaneous (subQ) injection is a common route for delivering biotherapeutics, wherein pharmacokinetics is largely influenced by drug transport in a complex subQ tissue microenvironment. The selection of good drug candidates with beneficial pharmacokinetics for subQ injections is currently limited by a lack of reliable testing models. To address this limitation, we report here a Subcutaneous Co-Culture Tissue-on-a-chip for Injection Simulation (SubCuTIS). SubCuTIS possesses a 3D coculture tissue architecture, and it allows facile quantitative determination of relevant scale independent drug transport rate constants. SubCuTIS captures key in vivo physiological characteristics of the subQ tissues, and it differentiates the transport behavior of various chemically distinct molecules. We supplemented the transport measurements with theoretical modeling, which identified subtle differences in the local absorption rate constants of seven clinically available mAbs. Accounting for first-order proteolytic catabolism, we established a mathematical framework to assess clinical bioavailability using the local absorption rate constants obtained from SubCuTIS. Taken together, the technology described here broadens the applicability of organs-on-chips as a standardized and easy-to-use device for quantitative analysis of subQ drug transport.
Phylogeny and classification of jumping plant lice of the subfamily Liviinae (Hemiptera: Psylloidea: Liviidae) based on molecular and morphological data
Authors: Burckhardt Daniel , Serbina Liliya Š , Malenovský Igor , Queiroz Dalva L , Aléné Désirée C , Cho Geonho , Percy Diana M 
Published: October 2023

Abstract
Using molecular (COI, Cytb, H3, wg, 12S, 16S, and 28S) and morphological data (61 characters of adults and immatures), the phylogenetic relationships of the 20 nominal genera of Liviinae were analysed, and the monophyly of the subfamily was tested relative to the other two subfamilies of Liviidae. The analyses of the molecular, morphological, and combined datasets provided similar results with a strong or moderate support in the molecular and combined analyses for the subfamilies of Liviidae and two clades in Liviinae given tribal rank (Liviini and Paurocephalini stat. rev.). Three of the six previously recognized genera were confirmed as monophyletic (Aphorma, Camarotoscena, and Livia) and three were shown to be polyphyletic: Diclidophlebia s.l. (Diclidophlebia s.s., Haplaphalara stat. rev., Klyveria Burckhardt, Serbina and Malenovský, gen. nov., Melanastera Serbina, Malenovský, Queiroz and Burckhardt, gen. nov. and Woldaia stat. rev.), Paurocephala s.l. (Liella Burckhardt, Serbina and Malenovský, gen. nov. and Paurocephala s.s.), and Syntomoza s.l. (Anomoterga stat. rev. and Syntomoza s.s.). The new generic definitions require 38 new and eight revived combinations, including the transfer of two species to other families. All genera of Liviinae are diagnosed and keys are provided for their identification. A checklist of world Liviinae is supplemented.
Defining chronic rejection in vascularized composite allografts – do we have reliable surrogates to look for?
Authors: Kanitakis Jean 
Published: October 2023

Purpose of review
Chronic rejection (CR) is a major threat in the field of vascularized composite tissue allografts (VCAs) as it causes graft dysfunction and usually graft loss. Unfortunately, knowledge of CR in VCA is incomplete because of the limited number of VCA recipients, the heterogeneous nature of VCAs and the short follow-up.

Recent findings
The diagnosis of CR in VCA has relied on clinical and pathological findings. Clinical changes include graft fibrosis, dyschromia and ischemic/necrotic ulcerations. Pathological changes primarily affect allograft vessels and manifest with graft vasculopathy (i.e. myo-intimal proliferation and luminal narrowing of allograft vessels, leading to graft ischemia). Attempts are made to diagnose CR with non- or minimally-invasive techniques, such as imaging studies (ultrasound biomicroscopy, functional magnetic resonance imaging) and serum biomarkers. These techniques provide interesting results and further insight into the mechanisms of CR in VCA.

Summary
The diagnosis of CR in VCA still relies mainly on clinicopathological graft alterations; unfortunately, these become overt rather late during the rejection process, when reversal of CR is problematic. More recent, minimally- or non-invasive techniques have provided encouraging results, but their usefulness in the diagnosis of CR requires further studies. These data highlight the paramount importance of CR prevention.
Novel Clinically Translatable Iron Oxide Nanoparticle for Monitoring Anti-CD47 Cancer Immunotherapy
Authors: Roudi Raheleh , Pisani Laura , Pisani Fabrizio , Kiru Louise , Daldrup-Link Heike E. 
Published: October 2023

Objectives
A novel clinically translatable iron oxide nanoparticle (IOP) is currently being tested in phase 2 clinical trials as a magnetic resonance imaging (MRI) contrast agent for hepatocellular carcinoma diagnosis. The purpose of our study is to evaluate if this IOP can detect activation of tumor-associated macrophages (TAMs) due to CD47 mAb-targeted immunotherapy in 2 mouse models of osteosarcoma.

Materials and Methods
The toxicity, biodistribution, and pharmacokinetics of IOP were evaluated in 77 female and 77 male rats. Then, 24 female BALB/c mice with intratibial murine K7M2 tumors and 24 female NOD scid gamma mice with intratibial human 143B osteosarcoma xenografts were treated with either CD47 mAb (n = 12) or control antibody (n = 12). In each treatment group, 6 mice underwent MRI scans before and after intravenous infusion of either IOP or ferumoxytol (30 mg Fe/kg). Tumor T2* values and TAM markers F4/80, CD80, CD206, and Prussian blue staining were compared between different experimental groups using exact 2-sided Wilcoxon rank sum tests.

Results
Biodistribution and safety evaluations of IOP were favorable for doses of less than 50 mg Fe/kg body weight in female and male rats. Both IOP and ferumoxytol caused negative enhancement (darkening) of the tumor tissue. Both murine and human osteosarcoma tumors treated with CD47 mAb demonstrated significantly shortened T2* relaxation times after infusion of IOP or ferumoxytol compared with controls (all P's < 0.05). Higher levels of F4/80+CD80+ were found in murine and human osteosarcomas treated with CD47 mAb compared with sham-treated controls (all P's < 0.05). In addition, murine CD47 mAb-treated tumors after infusion of either IOP or ferumoxytol showed significantly higher numbers of Prussian blue–positive cells compared with controls (P < 0.05). There was no significant difference of F4/80+CD206+ cells among any of the groups (all P's > 0.05).

Conclusions
Iron oxide nanoparticle–enhanced MRI can be used to diagnose CD47 mAb-mediated TAM-activation in osteosarcomas.
Metal Artifact Reduction in Photon-Counting Detector CT
Authors: Skornitzke Stephan , Mergen Victor , Biederer Jürgen , Alkadhi Hatem , Do Thuy D. , Stiller Wolfram , Frauenfelder Thomas , Kauczor Hans-Ulrich , Euler André 
Published: October 2023

Objectives
With the introduction of clinical photon-counting detector computed tomography (PCD-CT) and its novel reconstruction techniques, a quantitative investigation of different acquisition and reconstruction settings is necessary to optimize clinical acquisition protocols for metal artifact reduction.

Materials and Methods
A multienergy phantom was scanned on a clinical dual-source PCD-CT (NAEOTOM Alpha; Siemens Healthcare GmbH) with 4 different central inserts: water-equivalent plastic, aluminum, steel, and titanium. Acquisitions were performed at 120 kVp and 140 kVp (CTDIvol 10 mGy) and reconstructed as virtual monoenergetic images (VMIs; 110–150 keV), as T3D, and with the standard reconstruction “none” (70 keV VMI) using different reconstruction kernels (Br36, Br56) and with as well as without iterative metal artifact reduction (iMAR). Metal artifacts were quantified, calculating relative percentages of metal artifacts. Mean CT numbers of an adjacent water-equivalent insert and different tissue-equivalent inserts were evaluated, and eccentricity of metal rods was measured. Repeated-measures analysis of variance was performed for statistical analysis.

Results
Metal artifacts were most prevalent for the steel insert (12.6% average artifacts), followed by titanium (4.2%) and aluminum (1.0%). The strongest metal artifact reduction was noted for iMAR (with iMAR: 1.4%, without iMAR: 10.5%; P < 0.001) or VMI (VMI: 110 keV 2.6% to 150 keV 3.3%, T3D: 11.0%, and none: 16.0%; P < 0.001) individually, with best results when combining iMAR and VMI at 110 keV (1.2%). Changing acquisition tube potential (120 kV: 6.6%, 140 kV: 5.2%; P = 0.33) or reconstruction kernel (Br36: 5.5%, Br56: 6.4%; P = 0.17) was less effective. Mean CT numbers and standard deviations were significantly affected by iMAR (with iMAR: −3.0 ± 21.5 HU, without iMAR: −8.5 ± 24.3 HU; P < 0.001), VMI (VMI: 110 keV −3.6 ± 21.6 HU to 150 keV −1.4 ± 21.2 HU, T3D: −11.7 ± 23.8 HU, and none: −16.9 ± 29.8 HU; P < 0.001), tube potential (120 kV: −4.7 ± 22.8 HU, 140 kV: −6.8 ± 23.0 HU; P = 0.03), and reconstruction kernel (Br36: −5.5 ± 14.2 HU, Br56: −6.8 ± 23.0 HU; P < 0.001). Both iMAR and VMI improved quantitative CT number accuracy and metal rod eccentricity for the steel rod, but iMAR was of limited effectiveness for the aluminum rod.

Conclusions
For metal artifact reduction in PCD-CT, a combination of iMAR and VMI at 110 keV demonstrated the strongest artifact reduction of the evaluated options, whereas the impact of reconstruction kernel and tube potential was limited.
Outcomes of Decompressive Craniectomy in the Management of Traumatic Brain Injury: A Ten-Year Retrospective Analysis
Authors: Zeynal Mete , Akyüz Mehmet Emin 
Published: October 2023

Objective:
This study aimed to investigate factors associated with patient outcomes after decompressive craniectomy for severe traumatic brain injury (TBI) and to compare the authors’ findings with the existing literature.

Methods:
The authors conducted a retrospective analysis of 50 patients who underwent decompressive craniectomy for severe TBI between 2013 and 2023. Patient characteristics, including age, sex, Glasgow Coma Scale (GCS) score, Injury Severity Score (ISS), electrolyte imbalances, nosocomial infections, and hospital stay duration, were collected. Outcomes were assessed at 12 months postsurgery, and statistical analyses were performed to determine factors associated with favorable and unfavorable outcomes.

Results:
Younger age, higher GCS scores, and lower ISS were significantly associated with favorable outcomes. Electrolyte imbalances, particularly hyponatremia, and hyperkalemia, were linked to unfavorable outcomes. Nosocomial infections were significantly more common in patients with unfavorable outcomes. Longer hospital stays were also associated with worse outcomes.

Conclusions:
The authors’ findings highlight the importance of individualized patient management based on age, admission GCS score, ISS, electrolyte imbalances, nosocomial infections, and hospital stay duration to maximize the potential for favorable outcomes. These results contribute to the growing literature on decompressive craniectomy for TBI and provide valuable insights for clinicians in optimizing patient management.
Generating a Prioritised List of Operative Procedures for Simulation-Based Assessment of General Surgery Trainees through Consensus
Authors: Toale Conor , Morris Marie , Konge Lars , Nayahangan Leizl Joy , Roche Adam , Heskin Leonie , Kavanagh Dara O 
Published: October 2023

Objective:
to develop appropriate content for high-stakes simulation-based assessments of operative competence in general surgery training through consensus.

Summary Background Data:
Valid methods of summative operative competence assessment are required by competency-based training programmes in surgery.

Method:
An online Delphi consensus study was conducted. Procedures were derived from the competency expectations outlined by the Joint Commission on Surgical Training (JCST) curriculum 2021, and subsequent brainstorming. Procedures were rated according to their perceived importance, perceived procedural risk, how frequently they are performed, and feasibility, by a purposive sample of thirty surgical trainers and a five-person steering group. A modified Copenhagen Academy for Medical Education and Simulation Needs Assessment Formula (CAMES NAF) was applied to generated data in order to produce ranked procedural lists, which were returned to participants for re-prioritization.

Results:
Prioritised lists were generated for simulation-based operative competence assessments at two key stages of training; end of ‘phase 2’ prior to development of a sub-specialty interest, and end of ‘phase 3’ i.e. end-of-training certification. A total of 21 and 16 procedures were deemed suitable for assessments at each of these stages respectively.

Conclusions:
This study describes a national needs assessment approach to content generation for simulation-based assessments of operative competence in general surgery using Delphi consensus methodology. The prioritised procedural lists generated by this study can be used to further develop operative skill assessments for use in high-stakes scenarios such as trainee progression, entrustment and end-of-training certification prior to subsequent validity testing.
Liver-specific glucocorticoid action in alcoholic liver disease: study of glucocorticoid receptor knockout and knockin mice
Authors: Wang Yazheng , Lu Hong 
Published: October 2023

AbstractBackgroundGlucocorticoids are the only first-line drugs for severe alcoholic hepatitis (AH), with limited efficacy and various side effects on extrahepatic tissues. Liver-targeting glucocorticoid therapy may have multiple advantages over systemic glucocorticoid for AH. The purpose of this study was to determine the role of hepatocellular glucocorticoid receptor (GR) in alcoholic steatosis (AS) and AH.MethodsAS was induced by a high-fat diet plus binge alcohol in adult male and female mice with liver-specific knockout (LKO) and heterozygote of GR. AH was induced by chronic-plus-binge in middle-aged male mice with liver-specific knockin of GR. Changes in hepatic mRNA and protein expression were determined by qPCR and Western blot.ResultsGR LKO aggravated steatosis and decreased hepatic expression and circulating levels of albumin in both genders of AS mice but only increased markers of liver injury in male AS mice. Marked steatosis in GR LKO mice was associated with induction of lipogenic genes and down-regulation of bile acid synthetic genes. Hepatic protein levels of GR, hepatocyte nuclear factor 4α, and phosphorylated STAT3 were gene-dosage-dependently decreased, whereas that of lipogenic ATP citrate lyase was increased in male GR heterozygote and LKO mice. Interestingly, hepatic expression of estrogen receptor α (ERα) was induced, and the essential estrogen-inactivating enzyme sulfotransferase 1E1 was gene-dosage-dependently down-regulated in GR heterozygote and knockout AS mice, which was associated with induction of ERα-target genes. Liver-specific knockin of GR protected against liver injury and steatohepatitis in middle-aged AH mice.ConclusionsHepatocellular GR is important for protection against AS and AH.