bluuebunny/crossref_metadata_2025_split huggingface dataset:
Propeller Flap Reconstruction Following Pilonidal Cyst Excision
Authors: Towfighi Parhom , Huffman Samuel S. , Sayyed Adaah A. , Suvarnakar Aashka M. , Abdou Salma , Fitzgibbons Shimae C. , Drew Eleanor L. , Youn Richard C. , Kleiber Grant M. 
Published: June 2024

IntroductionReconstruction following pilonidal cyst resection must balance risk of recurrence, healing time, and resumption of functional routine. Propeller flaps provide a reliable and effective reconstructive option. This study highlights our experience with propeller flap reconstruction following pilonidal cyst resection and demonstrates the efficacy of same-day discharge.MethodsA single-institution retrospective chart review was performed for propeller flap reconstructions completed from March 2018 to July 2022. Patient demographics, pilonidal cyst details, operative details, and postoperative outcomes were collected. Primary outcomes included flap survival, flap complications, and pilonidal disease recurrence.ResultsTwenty-eight outpatient propeller flap reconstructions following pilonidal cyst resections were identified in 26 patients, with two patients receiving a second propeller flap due to recurrence. Most patients were male (n = 15, 57.7%) with a mean age at time of index operation of 25.5 ± 5.8 years and mean body mass index of 26.5 ± 4.1 kg/m2. Mean symptom duration prior to index surgery was 39.3 months. Mean skin defect size following resection was 28.3 ± 15.3 cm2, with a mean flap size of 44.7 ± 35.5 cm2. Flap survival was 100% (n = 28), with five flaps (17.9%) experiencing minor wound complications and one patient (3.8%) requiring return to the operating room. Mean time to functional improvement was 24.0 ± 22.8 days. Pilonidal disease recurrence occurred in three patients (11.5%). Mean follow-up was 4.1 ± 5.4 months.ConclusionsPropeller flaps provide a successful and reliable reconstructive option for pilonidal disease defects. Because patients in our cohort experienced favorable outcomes and functional improvement, we advocate for same-day discharge in order to reduce hospital and patient burden.
Acellular Dermal Matrix–Assisted, Prosthesis-Based Breast Reconstruction
Authors: Berger Lauren E. , Spoer Daisy L. , Huffman Samuel S. , Haffner Zoe K. , Tom Laura K. , Parkih Rajiv P. , Song David H. , Fan Kenneth L. 
Published: June 2024

BackgroundAcellular dermal matrices (ADMs) are frequently employed in immediate prosthesis-based breast reconstruction (iPBR) to provide structural support. Despite differences in ADM derivatives, few studies directly compare their outcomes in the setting of iPBR. We sought to conduct a large head-to-head study comparing 3 ADMs used across our institution.MethodsA multicenter retrospective review of patients undergoing iPBR with SurgiMend PRS (fetal bovine–derived; Integra Lifesciences, Princeton, NJ), AlloDerm (human-derived; LifeCell Corp, Bridgewater, NJ), or DermACELL (human-derived; Stryker Corp, Kalamazoo, MI) between January 2014 to July 2022 was performed. Primary outcomes included rates of unplanned explantation and total reconstructive failure. Secondary outcomes included 90-day postoperative complications and long-term rates of capsular contracture development.ResultsA total of 738 patients (1228 breasts) underwent iPBR during the study period; 405 patients received DermACELL (54.9%), 231 received AlloDerm (31.3%), and 102 received SurgiMend PRS (13.8%). Rates of short-term complications, total reconstruction failure, reoperation within 90 days, capsular contracture, and unplanned explantation were comparable. These findings remained true upon multivariate analysis accounting for baseline differences between cohorts, whereby ADM type was not an independent predictor of any outcome of interest. Conversely, factors such as body mass index, diabetes mellitus, smoking history, neoadjuvant and adjuvant chemotherapy, adjuvant radiation, skin-sparing mastectomy, Wise pattern and periareolar incisions, use of tissue expanders, and a subpectoral plane of insertion were significant predictors of postoperative complications.ConclusionLow rates of complications support the equivalency of fetal bovine and human-derived ADMs in iPBR. Patient characteristics and operative approach are likely more predictive of postoperative outcomes than ADM derivative alone.
Monodigital Double Cross-Finger Flaps—A Novel Approach for Coverage of Large Volar Defects
Authors: Kakola Mohan G. , N Vijaykumar , MS Chandrashekar 
Published: June 2024

Introduction
A single cross-finger flap can only address digital defects of a limited size, and larger defects often require distant flaps such as abdominal or groin flaps that are cumbersome to perform and sometimes bulky. Two cross-finger flaps harvested from the same donor digit could offer a simple and effective solution for many such defects. In this study, we describe the technique of monodigital double cross-finger flaps and its clinical applicability, with evaluation of donor and recipient site morbidity.

Methods and Materials
A total of 10 subjects with large volar defects were included in the study. The demographic data, etiology, defect size, flap donor, and recipient sites were tabulated prior to surgery. Each subject was assessed for postoperative complications at the donor and recipient site and followed up for 6–12 months to document any flap or donor site morbidities.

Results
The subjects included 9 males and 1 female subjects, with an average age of 35.6 years (21–67 years). Most patients had posttraumatic defects, with 3 cases of full thickness burns and one with postsurgical tissue necrosis. All defects were volar, with 4 on the little finger, 3, 2, and 1 in the ring, index and middle fingers, respectively. No major postoperative complications were noted in any case. All flaps survived well with good contour, and donor fingers achieved near-normal range of flexion with only minimal restriction (10–15°) at the distal interphalangeal joint that did not result in any overall functional disability.

Conclusions
Monodigital double cross-finger flap technique offers a simple and effective solution for reconstruction of large digital defects that are not amenable for closure by a classical cross-finger flap, and is a good alternative for other procedures, providing supple soft tissue coverage and no significant morbidity at the donor digit provided that there is preservation of a small skin bridge across the proximal interphalangeal joint.
FINDING THE SWEET SPOT: THE ASSOCIATION BETWEEN WHOLE BLOOD TO RED BLOOD CELLS RATIO AND OUTCOMES OF HEMORRHAGING CIVILIAN TRAUMA PATIENTS
Authors: Hosseinpour Hamidreza , Stewart Collin , Hejazi Omar , Okosun Stanley E. , Khurshid Muhammad Haris , Nelson Adam , Bhogadi Sai Krishna , Ditillo Michael , Magnotti Louis J. , Joseph Bellal 
Published: June 2024

ABSTRACTPurpose:To evaluate the dose-dependent effect of whole blood (WB) on the outcomes of civilian trauma patients with hemorrhagic shock.Methods:We performed a 2-year (2020–2021) retrospective analysis of the ACS-TQIP dataset. Adult (≥18) trauma patients with a shock index (SI) >1 who received at least 5 units of PRBC and one unit of WB within the first 4 h of admission were included. Primary outcomes were 6-h, 24-h, and in-hospital mortality. Secondary outcomes were major complications and hospital and intensive care unit length of stay.Results:A total of 830 trauma patients with a mean (SD) age of 38 (16) were identified. The median [IQR] 4-h WB and PRBC requirements were 2 [2–4] U and 10 [7–15] U, respectively, with a median WB:RBC ratio of 0.2 [0.1–0.3]. Every 0.1 increase in WB:RBC ratio was associated with decreased odds of 24-h mortality (aOR: 0.916,P= 0.035) and in-hospital mortality (aOR: 0.878,P< 0.001). Youden’s index identified 0.25 (1 U of WB for every 4 U of PRBC) as the optimal WB:PRBC ratio to reduce 24-h mortality. High ratio (≥0.25) group had lower adjusted odds of 24-h mortality (aOR: 0.678,P= 0.021) and in-hospital mortality (aOR: 0.618,P< 0.001) compared to the low ratio group.Conclusions:A higher WB:PRBC ratio was associated with improved early and late mortality in trauma patients with hemorrhagic shock. Given the availability of WB in trauma centers across the United States, at least one unit of WB for every 4 units of packed red blood cells may be administered to improve the survival of hemorrhaging civilian trauma patients.
Surgical Antimicrobial Prophylaxis in Low-Risk Cholecystectomies is Associated with Fewer Surgical Site Infections
Authors: Florinett Lena , Widmer Andreas , Troillet Nicolas , Beldi Guido , Von Flüe Markus , Harbarth Stephan , Sommerstein Rami ,   Swissnoso
Published: June 2024

Objective:
To assess whether administration of surgical antimicrobial prophylaxis (SAP) versus absence of SAP is associated with a decreased risk of surgical site infections (SSI) after low-risk cholecystectomies (LR-CCE).

Summary Background Data:
Current guidelines do not recommend routine SAP administration prior to LR-CCE.

Methods:
This cohort study included adult patients who underwent LR-CCE and were documented by the Swissnoso SSI surveillance system between 1/2009-12/2020 at 66 Swiss hospitals. LR-CCE was specified as elective endoscopic surgery, age <70, no active cholecystitis, ASA score <3, operating time <120 minutes without implantation of foreign material. Exposure was defined as the administration of cefuroxime or cefazoline ± metronidazole within 120 minutes prior to incision versus no SAP administration. Our main outcome was occurrence of SSI until day 30. Logistic regression models were used to adjust for institutional, patient, and perioperative variables.

Results:
Of 44 682 surveilled adult cholecystectomy patients, 12 521 (8 726 women [69.7%]; median [IQR] age, 49.0 [38.1-58.2] years), fulfilled inclusion criteria. SSI was identified in 143 patients (1.1%). SAP was administered in 9 269 patients (74.0%) and was associated with a lower SSI rate (adjusted odds ratio [aOR], 0.50; 95% CI, 0.35-0.70; P < 0.001). The number needed to treat to prevent one SSI episode is 100.

Conclusions:
The overall LR-CCE SSI rate was 1.1%. SAP was associated with a 50% lower overall SSI rate. Patients undergoing LR-CCE may benefit from routine surgical antimicrobial prophylaxis.
Nocardioides agri sp. nov., isolated from garden soil
Authors: Huq Md. Amdadul , NAM Kihong , Rahman Md. Shahedur , Rahman M. Mizanur , Parvez Md. Anowar Khasru , Kang Kwon-Kyoo , Akter Shahina 
Published: June 2024

A novel bacterial strain, designated as MAH-18T, was isolated from soil sampled in a flower garden. Cells of strain MAH-18T were Gram-stain-positive, aerobic, motile, and rod-shaped. The colonies were beige in colour, smooth, and spherical when grown on Reasoner's 2A agar medium. Strain MAH-18T grew at 20–40 °C, pH 6.0–8.0, and 0–1.0 % NaCl. Cells were able to hydrolyse aesculin, gelatin, and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was determined to be a member of the genus Nocardioides and most closely related to Nocardioides pyridinolyticus OS4T (97.9 %), Nocardioides hankookensis DS-30T (97.9 %), Nocardioides aquiterrae GW-9T (97.6 %), Nocardioides soli mbc-2T (97.5 %), Nocardioides conyzicola HWE 2-02T (97.4 %), and Nocardioides mangrovi GBK3QG-3T (96.3 %). Strain MAH-18T has a draft genome size of 4 788 325 bp (eight contigs), 4572 protein-coding genes, 46 tRNA, and three rRNA genes. The average nucleotide identity and digital DNA–DNA hybridization values between strain MAH-18T and the closest type strains were 81.5–83.4 % and 24.4–25.8 %, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAH-18T. The G+C content of the genomic DNA of strain was 72.2 mol% and the predominant isoprenoid quinone was MK-8 (H4). The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, and unknown phospholipids. The major cellular fatty acids were determined to be C16:0 iso and C17 : 1
ω6c. The DNA–DNA hybridization results and phenotypic, genotypic, and chemotaxonomic data demonstrated that strain MAH-18T represents a novel species, for which the name Nocardioides agri sp. nov. is proposed, with MAH-18T as the type strain (=KACC 19744T=CGMCC 1.13656T).
Hwangdonia lutea sp. nov., isolated from the Haima cold seep, South China Sea
Authors: Huang Qinyu , Lyu Lina , Li Qiqi , Su Hongfei , Li Jie 
Published: June 2024

A Gram-stain-negative, orange-yellow, rod-shaped bacterium, designated strain SCSIO 19198T, was isolated from sediment of the Haima cold seep in the South China Sea, PR China. The strain was aerobic and non-motile. Growth of strain SCSIO 19198T occurred at pH 7–9 (optimum, pH 7), 15–37 °C (optimum, 25–32 °C) and with 3–8 % (w/v) NaCl (optimum, 3–6 % NaCl). Phylogenetic analyses based on 16S rRNA sequences revealed that strain SCSIO 19198T belonged to the genus Hwangdonia, having the highest similarity to Hwangdonia seohaensis HD-3T (98.35 %), followed by Algibacter aquimarinus KYW589T (95.17 %) and Gelatiniphilus marinus GYP-24T (94.89 %). The DNA G+C content was 35.92 mol%. The average nucleotide identity value between the genome of strain SCSIO 19198T and that of H. seohaensis HD-3T was 88.49 %. The digital DNA–DNA hybridization value between strain SCSIO 19198T and H. seohaensis HD-3T was 36 %. The major fatty acids (>10 %) of strain SCSIO 19198T were iso-C15 : 0, iso-C15 : 1 G, summed feature 3 (C16 : 1
ω6c/C16 : 1 ω7c) and anteiso-C15 : 0. MK-6 was the only detected respiratory quinone. The polar lipids of strain SCSIO 19198T included phosphatidylethanolamine, two aminolipids, glycolipid and two unidentified lipids. The phenotypic, phylogenetic, chemotaxonomic and genomic data clearly suggest that strain SCSIO 19198T represents a novel species of the genus Hwangdonia, for which the name Hwangdonia lutea sp. nov. is proposed. The type strain is SCSIO 19198T (=MCCC 1K08674T=KCTC 102078T).
Autofluorescence Virtual Staining System for H&E Histology and Multiplex Immunofluorescence Applied to Immuno-Oncology Biomarkers in Lung Cancer
Authors: Loo Jessica , Robbins Marc , McNeil Carson , Yoshitake Tadayuki , Santori Charles , Shan Chuanhe (Jay) , Vyawahare Saurabh , Patel Hardik , Wang Tzu Chien , Findlater Robert , Steiner David F. , Rao Sudha , Gutierrez Michael , Wang Yang , Sanchez Adrian C. , Yin Raymund , Velez Vanessa , Sigman Julia S. , Coutinho de Souza Patricia , Chandrupatla Hareesh , Scott Liam , Weaver Shamira S. , Lee Chung-Wein , Rivlin Ehud , Goldenberg Roman , Couto Suzana S. , Cimermancic Peter , Wong Pok Fai 
Published: June 2024

AbstractVirtual staining for digital pathology has great potential to enable spatial biology research, improve efficiency and reliability in the clinical workflow, as well as conserve tissue samples in a non-destructive manner. In this study, we demonstrate the feasibility of generating virtual stains for hematoxylin and eosin (H&E) and a multiplex immunofluorescence (mIF) immuno-oncology panel (DAPI, PanCK, PD-L1, CD3, CD8) from autofluorescence images of unstained non-small cell lung cancer tissue by combining high-throughput hyperspectral fluorescence microscopy and machine learning. Using domain-specific computational methods, we evaluated the accuracy of virtual H&E for histologic subtyping and virtual mIF for cell segmentation-based measurements, including clinically-relevant measurements such as tumor area, T cell density, and PD-L1 expression (tumor proportion score and combined positive score). The virtual stains reproduce key morphologic features and protein biomarker expressions at both tissue and cell levels compared to real stains, enable the identification of key immune phenotypes important for immuno-oncology, and show moderate to good performance across various evaluation metrics. This study extends our previous work on virtual staining from autofluorescence in liver disease and prostate cancer, further demonstrating the generalizability of this deep learning technique to a different disease (lung cancer) and stain modality (mIF).SignificanceWe extend the capabilities of virtual staining from autofluorescence to a different disease and stain modality. Our work includes newly developed virtual stains for H&E and a multiplex immunofluorescence panel (DAPI, PanCK, PD-L1, CD3, CD8) for non-small cell lung cancer, which reproduce the key features of real stains.
Cleaning the Dead: Optimized decontamination enhances palaeoproteomic analyses of Pleistocene skeletal material
Authors: Fagernäs Zandra , Villa Islas Viridiana , Troché Gaudry , Buylaert Jan-Pieter , Khujageldiev Tura , Kurbanov Redzhep , Olsen Jesper V. , Pedersen Mikkel Winther , Welker Frido 
Published: June 2024

AbstractThe study of ancient proteins preserved in a range of archaeological, cultural heritage, and palaeontological materials is increasingly contributing to our understanding of human evolution and archaeological research questions. Many of the specimens studied have been excavated and stored for a significant duration prior to their proteomic analysis. Human handling and storage environments therefore provide ample opportunities for protein contamination onto and into specimens of interest to palaeoproteomic studies. As such, modern protein contamination limits access to endogenous proteomes. Here, we compare five approaches of bone protein decontamination applied to a PleistoceneEquussp. bone fragment contaminated with a modern dog salivary proteome. We find that all tested methods reduce the protein contamination, but with different efficiencies. We find that a brief bleach wash is the most effective approach in removing modern protein contamination, and that no additional damage is caused to the endogenous proteome by this treatment. Next, we apply this approach to a hominin tooth found at Khudji, a Late Pleistocene archaeological site in Tajikistan. We demonstrate that a brief bleach wash removes almost all human skin protein contamination while retaining the endogenous hominin dentine proteome. Subsequent phylogenetic analysis of the Khudji dentine proteome allowed determination that the specimen is likely not a Denisovan, but still leaves ambiguity between an assignment to either modern humans or Neanderthals.
Chromatin enables precise and scalable gene regulation with factors of limited specificity
Authors: Perkins Mindy Liu , Crocker Justin , Tkačik Gašper 
Published: June 2024

Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone, and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.Significance StatementReliably keeping a gene off is as important as controlling its expression level when the gene is on. Yet both tasks become challenging in the packed nuclear environment of a eukaryotic cell, where the numerous and diverse regulatory proteins that are present cannot bind enhancers for target genes with perfect specificity. While regulatory schemes based on prokaryotic models would be overwhelmed by errors in such conditions, we show that chromatin-based regulation, an evolutionary innovation of eukaryotic cells, successfully rescues precise gene expression control by reliably keeping desired genes off. Our systems-level computational analysis demonstrates that this result is nontrivial, because chromatin opening must itself be correctly regulated. We furthermore identify when and how chromatin-based regulation outperforms alternative schemes.
Flavonoid metabolism and its different physiological roles in plant cold acclimation
Authors: Kitashova Anastasia , Lehmann Martin , Schwenkert Serena , Leister Dario , Nägele Thomas 
Published: June 2024

AbstractFlavonoids represent a diverse group of plant secondary metabolites which are also discussed in context of dietary health and inflammatory response. Numerous studies have revealed that flavonoids play a central role in plant acclimation to abiotic factors like low temperature or high light, but their structural and functional diversity frequently prevents a detailed mechanistic understanding. Further complexity in analysing flavonoid metabolism arises from the different subcellular compartments which are involved in biosynthesis and storage. In the present study, non-aqueous fractionation ofArabidopsisleaf tissue was combined with metabolomics and proteomics analysis to reveal subcellular regulation during cold acclimation in two flavonoid-deficient mutants. During the first three days of a two-week cold acclimation period, flavonoid deficiency was observed to affect pyruvate, citrate and glutamate metabolism which indicated a role in stabilising C/N metabolism and photosynthesis. Also, tetrahydrofolate metabolism was found to be affected which had significant effects on regulation of the proteome of the photorespiratory pathway. In the late stage of cold acclimation, flavonoid deficiency was found to affect protein stability, folding and proteasomal degradation which resulted in a significant decrease of total protein amounts in both mutants. In summary, these findings suggest that flavonoid metabolism plays different roles in early and late stages of plant cold acclimation and significantly contributes to establishing a new protein homeostasis in a changing environment.