bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isotropic gap formation, localization, and waveguiding in mesoscale Yukawa-potential amorphous structures
Authors: Sarihan Murat Can , Govdeli Alperen , Lan Zhihao , Yilmaz Yildirim Batuhan , Erdil Mertcan , Wang Yupei , Aras Mehmet Sirin , Yanik Cenk , Panoiu Nicolae Coriolan , Wong Chee Wei , Kocaman Serdar 
Published: January 2024

AbstractAmorphous photonic structures are mesoscopic optical structures described by electrical permittivity distributions with underlying spatial randomness. They offer a unique platform for studying a broad set of electromagnetic phenomena, including transverse Anderson localization, enhanced wave transport, and suppressed diffusion in random media. Despite this, at a more practical level, there is insufficient work on both understanding the nature of optical transport and the conditions conducive to vector-wave localization in these planar structures, as well as their potential applications to photonic nanodevices. In this study, we fill this gap by investigating experimentally and theoretically the characteristics of optical transport in a class of amorphous photonic structures and by demonstrating their use to some basic waveguiding nanostructures. We demonstrate that these 2-D structures have unique isotropic and asymmetric band gaps for in-plane propagation, controlled from first principles by varying the scattering strength and whose properties are elucidated by establishing an analogy between photon and carrier transport in amorphous semiconductors. We further observe Urbach band tails in these random structures and uncover their relation to frequency- and disorder-dependent Anderson-like localized modes through the modified Ioffe-Regel criterion and their mean free path - localization length character. Finally, we illustrate that our amorphous structures can serve as a versatile platform in which photonic devices such as disorder-localized waveguides can be readily implemented.
Complications Following Gender-Affirming Phalloplasty: A NSQIP Review
Authors: Hassan Bashar , Brown Madyson , Guo Lily , Ascha Mona , Jedrzejewski Breanna , Cohen Andrew , Corral Gabriel Del , Liang Fan 
Published: January 2024

Abstract
Background Gender-affirming phalloplasty has a complication rate as high as 76.5%. This is the first study to determine the predictors of 30-day complications following phalloplasty using a national registry.
Methods The National Surgical Quality Improvement Program database (2012–2021) was queried for transgender men and Current Procedural Terminology codes pertaining to flap or microsurgery procedures to select for single- and first-stage phalloplasty cases. Included were patients with a length of total hospital stay ≥ 5 days and operating time > 4 hours to select for primary phalloplasty cases. The primary outcome was incidence of major and minor complications, and the secondary outcome was indication for unplanned reoperation. Bivariate analysis and multivariate logistic regression were performed to determine significant predictors of complications.
Results Of 90 patients, 18 (20.0%) patients developed at least one complication. The most common complication was unplanned reoperation (n = 10, 11.1%) due to hematoma evacuation (n = 3, 30.0% of reoperations, 3.3% of all patients). A total of 43 (47.8%) underwent single-stage phalloplasty, and 47 (52.2%) underwent first-stage phalloplasty. Compared with patients without complications, those with minor complications are more likely to have had single-stage phalloplasty (n = 37 [45.1%], n = 6 [75.0%]; p = 0.145), but the association was not statistically significant. Longer operating time was associated with greater odds of major complications (adjusted odds ratio [aOR] 95% confidence interval [CI] 1.01 [1.002–1.018]). Patients who smoked within 1 year of surgery had 123 times the odds of 30-day minor complications (surgical site infection, urinary tract infection, wound dehiscence, pneumonia) compared with nonsmokers (aOR [CI] 123.3 [1.4– > 100.0]).
Conclusion There were no significant differences in complication rates between single- and first-stage phalloplasties. Patients should be counseled about the overall risk of 30-day complications following phalloplasty. Reducing operating time, smoking cessation, and strict preoperative nicotine testing may assist in mitigating odds of 30-day complications following phalloplasty.
Techniques and Outcomes in Microsurgical Treatment of Posttraumatic Lymphedema: A Systematic Review
Authors: Dahl Victoria A. , Tadisina Kashyap K. , Hale Eva , Fullerton Natalia , Mella-Catinchi Juan , Xu Kyle Y. 
Published: January 2024

Abstract
Background The microsurgical treatment of lymphedema has been well-studied and has been shown to be effective, especially in cancer-related lymphedema. Posttraumatic lymphedema (PTL) is a debilitating condition that remains understudied and underreported, and surgical techniques for PTL treatment are not well-represented in the literature. The purpose of this study was to systematically review all published reports of physiologic surgical interventions for PTL.
Methods A search was conducted on PubMed, MEDLINE, Embase, and Web of Science, from January 1, 2000 to December 6, 2022, using keywords “PTL,” “lymphedema,” and “surgery” to identify reports of PTL treated with microsurgical lymphatic reconstruction techniques. PTL cases treated with ablation, debulking, or decongestive therapy were excluded.
Results A total of 18 records that met the inclusion criteria were identified, representing 112 patients who underwent microsurgical operations for PTL. This included 60 cases of lymph flow restoration (LFR) via lymph axiality and interpositional flap transfer, 29 vascularized lymph node transfers, 11 lymphatic vessel free flaps, 10 lymphovenous anastomoses (LVAs), and 2 autologous lymphovenous transfers. Outcomes were primarily reported as clinical improvement or LFR by lymphatic imaging. All studies showed qualitative improvement of symptoms and reports with quantitative data showed statistically significant improvements.
Conclusion PTL is currently underrepresented in lymphedema treatment literature, however, our results show that microsurgical techniques are successful in treating lymphedema in PTL patients. Increasing awareness of PTL and establishing standardized diagnostic criteria and treatment options will help clinicians better understand how to diagnose and treat this condition. Prospective and comparative studies are needed to determine true prevalence of PTL and optimal treatment strategies.
Global environmental impacts of food system from regional shock: Russia-Ukraine war as an example
Authors: Zhang Haoran , Jiao Limin , Li Cai , Deng Zhongci , Wang Zhen , Jia Qiqi , Lian Xihong , Liu Yaolin , Hu Yuanchao 
Published: January 2024

AbstractDifferent responses to external interference, such as regional conflict, could have distinct sustainability outcomes. Here, we developed a novel framework to examine global food shortages from the Russia-Ukraine conflict and quantify the embodied environmental impacts of disturbed and alternative food supply chains. The conflict could soon bring a 50–120 Mt shortage of nine dominant food products and cause temporal global cropland abandonment and greenhouse gas emissions decline. By contrast, the partial agricultural recovery in the next cultivation season will raise global cropland use and greenhouse gas emissions by 9–10% and 2–4% (mainly in China and Europe). However, optimized food supply networks with prioritized agricultural expansion in higher-efficiency countries could minimize food shortages and food-mile expenses, offsetting the postwar environmental increments from agricultural recovery by 45–89%. These results validate a framework to simulate the global social-ecological system, and underline the resistance opportunities and tele-connected consequences of regional disturbance.
Manipulating ionic conductivity through chemical modifications in solid-state electrolytes prepared with binderless laser powder bed fusion processing
Authors: Acord Katherine A , Dupuy Alexander D , Chen Qian Nataly , Schoenung Julie M 
Published: January 2024

Abstract
Additive manufacturing of solid-state batteries is advantageous for improving the power density by increasing the geometric complexity of battery components, such as electrodes and electrolytes. In the present study, bulk three-dimensional Li1+x
Al
x
Ti2−x
(PO4)3 (LATP) electrolyte samples were prepared using the laser powder bed fusion (L-PBF) additive manufacturing method. Li3PO4 (LPO) was added to LATP to compensate for lithium vaporization during processing. Chemical compositions included 0, 1, 3, and 5 wt. % LPO. Resulting ionic conductivity values ranged from 1.4 × 10−6–6.4 × 10−8 S cm−1, with the highest value for the sample with a chemical composition of 3 wt. % LPO. Microstructural features were carefully measured for each chemical composition and correlated with each other and with ionic conductivity. These features and their corresponding ranges include: porosity (ranging from 5% to 19%), crack density (0.09–0.15 mm mm−2), concentration of residual LPO (0%–16%), and concentration and Feret diameter of secondary phases, AlPO4 (11%–18%, 0.40–0.61 µm) and TiO2 (9%–11%, 0.50–0.78). Correlations between the microstructural features and ionic conductivity ranged from −0.88 to 0.99. The strongest negative correlation was between crack density and ionic conductivity (−0.88), confirming the important role that processing defects play in limiting the performance of bulk solid-state electrolytes. The strongest positive correlation was between the concentration of AlPO4 and ionic conductivity (0.99), which is attributed to AlPO4 acting as a sintering aid and the role it plays in reducing the crack density. Our results indicate that additions of LPO can be used to balance competing microstructural features to design bulk three-dimensional LATP samples with improved ionic conductivity. As such, refinement of the chemical composition offers a promising approach to improving the processability and performance of functional ceramics prepared using binderless, laser-based additive manufacturing for solid-state battery applications.
ML-based regionalization of climate variables to forecast seasonal precipitation for water resources management
Authors: Lee Taesam , Won Chang-Hee , Singh Vijay P 
Published: January 2024

Abstract
Numerous dams and reservoirs have been constructed in South Korea, considering the distribution of seasonal precipitation which highly deviates from the actual one with high precipitation amount in summer and very low amount in other seasons. These water-related structures should be properly managed in order to meet seasonal demands of water resources wherein the forecasting of seasonal precipitation plays a critical role. However, owing to the impact of diverse complex weather systems, seasonal precipitation forecasting has been a challenging task. The current study proposes a novel procedure for forecasting seasonal precipitation by: (1) regionalizing the influential climate variables to the seasonal precipitation with k-means clustering; (2) extracting the features from the regionalized climate variables with machine learning-based algorithms such as principal component analysis (PCA), independent component analysis (ICA), and Autoencoder; and (3) finally regressing the extracted features with one linear model of generalized linear model (GLM) and another nonlinear model of support vector machine (SVM). Two globally gridded climate variables-mean sea level pressure (MSLP) and sea surface temperature (SST)-were teleconnected with the seasonal precipitation of South Korea, denoted as accumulated seasonal precipitation (ASP). Results indicated that k-means clustering successfully regionalized the highly correlated climate variables with the ASP, and all three extraction algorithms-PCA, ICA, and Autoencoder-combined with the GLM and SVM models presented their superiority in different seasons. In particular, the PCA combined with the linear GLM model performed better, and the Autoencoder combined with the nonlinear SVM model did better. It can be concluded that the proposed forecasting procedure of the seasonal precipitation, combined with several ML-based algorithms, can be a good alternative.
PERFUMES: pipeline to extract RNA functional motifs and exposed structures
Authors: Chol Arnaud , Sarrazin-Gendron Roman , Lécuyer Éric , Blanchette Mathieu , Waldispühl Jérôme 
Published: January 2024

Abstract

Motivation
Up to 75% of the human genome encodes RNAs. The function of many non-coding RNAs relies on their ability to fold into 3D structures. Specifically, nucleotides inside secondary structure loops form non-canonical base pairs that help stabilize complex local 3D structures. These RNA 3D motifs can promote specific interactions with other molecules or serve as catalytic sites.

Results
We introduce PERFUMES, a computational pipeline to identify 3D motifs that can be associated with observable features. Given a set of RNA sequences with associated binary experimental measurements, PERFUMES searches for RNA 3D motifs using BayesPairing2 and extracts those that are over-represented in the set of positive sequences. It also conducts a thermodynamics analysis of the structural context that can support the interpretation of the predictions. We illustrate PERFUMES’ usage on the SNRPA protein binding site, for which the tool retrieved both previously known binder motifs and new ones.

Availability and implementation
PERFUMES is an open-source Python package (https://jwgitlab.cs.mcgill.ca/arnaud_chol/perfumes).
Energy and exergy analysis of a 20-MW grid-connected PV plant operating under harsh climatic conditions
Authors: Aoun Nouar 
Published: January 2024

Abstract
Large grid-connected photovoltaic (PV) plants are increasingly being installed around the world, including in harsh desert climates. Evaluating their performance can help improve the design and operation of PV systems. This study performed an energy and exergy analysis of a 20-MW grid-connected PV plant under desert climatic conditions in southern Algeria over a period of 1 year. The PV plant was divided into two 10-MW subsystems. Energy analysis was performed using actual irradiation, power output, wind speed and ambient temperature data. The annual average energy efficiency of the plant and subsystems was 10.82%, 10.95% and 10.69%, respectively. Solar radiation had the most significant impact (80% determination coefficient) on thermal exergy loss. The exergy efficiency of the plant was lower than the literature values, likely due to the harsh desert conditions. The comprehensive energy and exergy analysis provides insights into the performance of large-scale PV plants in desert climates. The results can help guide the system design and operation improvements for such conditions. Regular cleaning and cooling could improve performance.
Target flow deviations on the cardiopulmonary bypass cause postoperative delirium in cardiothoracic surgery—a retrospective study evaluating temporal fluctuations of perfusion data
Authors: Krefting Johannes , Gorki Hagen , Hoenicka Markus , Albrecht Günter , Kraft Robert , Liebold Andreas 
Published: January 2024

Abstract

OBJECTIVES
Postoperative delirium (POD) is common, costly and associated with long-term morbidity and increased mortality. We conducted a cohort study to assess the contribution of cardiopulmonary bypass (CPB) to the development of POD by means of algorithm-based data processing.

METHODS
A database was compiled from 3 datasets of patients who underwent cardiac surgery between 2014 and 2019: intensive care unit discharge files, CPB protocols and medical quality management records. Following data extraction and structuring using novel algorithms, missing data were imputed. Ten independent imputations were analysed by multiple logistic regression with stepwise deletion of factors to arrive at a minimal adequate model.

RESULTS
POD was diagnosed in 456/3163 patients (14.4%). In addition to known demographic risk factors and comorbidities like male sex, age, carotid disease, acute kidney failure and diabetes mellitus, cardiopulmonary parameters like total blood volume at the CPB [adjusted odds ratio (AOR) 1.001; confidence interval (CI) 1.1001–1.002] were independent predictors of POD. Higher values of the minimal blood flow were associated with a lower risk of POD (AOR 0.993; CI 0.988–0.997). Flow rates at least 30% above target did emerge in the minimal adequate model as a potential risk factor, but the confidence interval suggested a lack of statistical significance (AOR 1.819; 95% CI: 0.955–3.463).

CONCLUSIONS
CPB data processing proved to be a useful tool for obtaining compact information to better identify the roles of individual operational states. Strict adherence to perfusion limits along with tighter control of blood flow and acid–base balance during CPB may help to further decrease the risk of POD.
Differential Abundances of Bdellovibrio and Rheinheimera in the Oral Microbiota of Neonates With and Without Clinical Sepsis
Authors: Thatrimontrichai Anucha , Surachat Komwit , Singkhamanan Kamonnut , Thongsuksai Paramee 
Published: January 2024

Background:
Neonatal sepsis is associated with high rates of morbidity and mortality, long hospital stays and high cost of care, thereby inflicting a burden on health care systems. Oral care with breast milk has been shown to modify the intestinal tract microbiota and immune system. Herein, we attempted to identify probiotics that may be beneficial to prevent or treat neonatal sepsis.

Methods:
This was a secondary analysis comparing the microbiota during oropharyngeal care in very-low-birth-weight infants with and without clinical sepsis. Oral samples were collected before oral feeding was initiated. The primary outcome was oral microbiota composition including diversity, relative abundance and linear discriminant analysis effect size.

Results:
Sixty-three neonates, including 39 and 24 with and without clinical sepsis, respectively, were enrolled. The medians gestational age and birth weight were 29 (27–30) weeks and 1010 (808–1263) g. Neonates with clinical sepsis had lower gestational age, birth weight (both P < 0.001) and lower rate of oral care with breast milk (P = 0.03), but higher doses and days of antibiotic exposure (both P < 0.001) compared to neonates without clinical sepsis. No differences in alpha and beta diversities were found between groups and Streptococcus agalactiae was the most common bacteria in both groups. Linear discriminant analysis effect size analysis revealed that neonates without clinical sepsis had significantly higher abundances of order Bdellovibrionales, family Bdellovibrionaceae, genus Bdellovibrio and genus Rheinheimera.

Conclusions:
Neonates without clinical sepsis had a significantly greater abundance of the Bdellovibrio and Rheinheimera genera.
RNA-sequencing of Human Kidney Allografts and Delineation of T-Cell Genes, Gene Sets, and Pathways Associated With Acute T Cell–mediated Rejection
Authors: Mueller Franco B. , Yang Hua , Li Carol , Dadhania Darshana M. , Xiang Jenny Z. , Salvatore Steven P. , Seshan Surya V. , Sharma Vijay K. , Suthanthiran Manikkam , Muthukumar Thangamani 
Published: January 2024

Background.
Delineation of T-cell genes, gene sets, pathways, and T-cell subtypes associated with acute T cell–mediated rejection (TCMR) may improve its management.

Methods.
We performed bulk RNA-sequencing of 34 kidney allograft biopsies (16 Banff TCMR and 18 no rejection [NR] biopsies) from 34 adult recipients of human kidneys. Computational analysis was performed to determine the differential intragraft expression of T-cell genes at the level of single-gene, gene set, and pathways.

Results.
T-cell signaling pathway gene sets for plenary T-cell activation were overrepresented in TCMR biopsies compared with NR biopsies. Heightened expression of T-cell signaling genes was validated using external TCMR biopsies. Pro- and anti-inflammatory immune gene sets were enriched, and metabolism gene sets were depleted in TCMR biopsies compared with NR biopsies. Gene signatures of regulatory T cells, Th1 cells, Th2 cells, Th17 cells, T follicular helper cells, CD4 tissue-resident memory T cells, and CD8 tissue-resident memory T cells were enriched in TCMR biopsies compared with NR biopsies. T-cell exhaustion and anergy were also molecular attributes of TCMR. Gene sets associated with antigen processing and presentation, and leukocyte transendothelial migration were overexpressed in TCMR biopsies compared with NR biopsies. Cellular deconvolution of graft infiltrating cells by gene expression patterns identified CD8 T cell to be the most abundant T-cell subtype infiltrating the allograft during TCMR.

Conclusions.
Our delineation of intragraft T-cell gene expression patterns, in addition to yielding new biological insights, may help prioritize T-cell genes and T-cell subtypes for therapeutic targeting.
BOLDsωimsuite: A new software suite for forward modeling of the BOLD fMRI signal
Authors: Chausse Jacob , Berman Avery J. L. , Chen J. Jean 
Published: January 2024

AbstractIn trying to elucidate the mechanisms of the blood-oxygenation level-dependent (BOLD) functional MRI (fMRI) techniques and to expand on the potential of the transverse relaxation time (T2*) in quantitative MRI, many methods for the forward modelling of the BOLD effect have been created and analyzed. Simulations of this nature can be difficult to implement without prior experience, and differences made by methodological choices can be unclear, which provides a significant barrier of entry into the field. In this paper, we present BOLDswimsuite, a toolbox for forward modeling of the BOLD effect, which collects many of the principal methods used in the literature into a single coherent package. Implemented as a Python package, simulations are built-in scripts by combining various simulation components, while providing flexibility in methodological choices. The goal of this toolbox is to provide an open-source, reproducible software suite that is adaptable for simulations in different MRI applications, and to which additional features can be added by the user with relative ease. This paper first provides an overview of the methods available in the package and how these methods can be constructed from the toolbox’s modular code components. Then, a brief theoretical explanation of each simulation component is given, supported by the relevant contributors. Next, sample simulations and analyses that can be created using the package are presented to display its features. Finally, recommendations regarding computational requirements are included to help users choose the best simulation methods to fit their needs. This package has many use cases and significantly reduces methodological barriers to forward modeling. It can also be a good learning tool for MR physics as well as a powerful tool to promote reproducible science.