bluuebunny/crossref_metadata_2025 huggingface dataset:
RADT-04. ASSESSMENT OF CLINICAL AND NEUROLOGICAL ALTERATIONS BEFORE RADIATION THERAPY IN CHILDREN WITH MALIGNANT BRAIN TUMORS
Authors: Lecchi Mara , Erbetta Alessandra , Cavatorta Claudia , Nigro Olga , Oprandi Chiara Maria , Pecori Emilia , Biassoni Veronica , Schiavello Elisabetta , Grampa Paolo , Meroni Silvia , Nigri Anna , Peruzzo Denis , Alessandro Ombretta , Laureanti Rita , Mainardi Luca , Vennarini Sabina , Poggi Geraldina , Pignoli Emanuele , Verderio Paolo , Massimino Maura
Published: June 2024

BACKGROUND

Young patients with malignant brain tumors show neurocognitive alterations as both consequences of the tumor and of treatments received. A prospective study of longitudinal radiation damages after focal RT was activated in 2017. We present the first analysis correlating tumor localization, symptoms, neurological/endocrinological impairments, surgery/ies if adopted, and cognitive assessments at the time of enrollment.

METHODS

Sixty-six children eligible for focal RT were enrolled and underwent a neurocognitive assessment based on standardized tests (“impaired”/“non-impaired”). The database included demographical, clinical and pathological variables. The latter, together with MRI morphological scans, were used to define different kind of damage scores. The pattern of associations between clinical variables and damage scores was investigated.

RESULTS

Patients median age was 8 years; the most frequent tumor was Ependymoma (41%) and Posterior Fossa (29%) was the prevalent tumor site. All but 5 children (with Germ Cell Tumors), had undergone surgery and 32 had undergone chemotherapy before irradiation and evaluations. Ad-hoc scores of neurological deficits and endocrine alterations were created to characterize each patient. Moreover, structural abnormalities were quantified in a score for each cortical/subcortical region. Patients with posterior fossa Ependymomas and infratentorial tumors showed higher neurological damage scores. Endocrine alterations were more serious in supratentorial tumors, specifically in patients with Craniopharyngioma and Germ Cell tumors of the sellar region and ventricular system. Deficit scores were not associated to the presence of hydrocephalus and surgery, unlike endocrine alteration scores. The median number of child’s structural damaged areas was equal to 2 (IQR: 2-3). Tumor sites of patients with an impaired or non-impaired full-scale IQ or visual-perception index, was found to be different.

CONCLUSIONS

The analysis of baseline evaluations highlights damages preexisting to irradiations and generated by multiple factors. In light of these findings, damages over time could be better investigated by distinguishing multiple generating factors.
Meeting the Therapeutic Challenges of Emergent and Rare Invasive Fungal Diseases Through Novel Clinical Trial Designs
Authors: Walsh Thomas J
Published: June 2024

Treatments for emerging and rare invasive fungal diseases (IFDs) represent a critical unmet medical need. For IFDs that occur less frequently than invasive aspergillosis, such as mucormycosis, hyalohyphomycosis, and phaeohyphomycosis, randomized controlled clinical trials are impractical and unlikely to meet urgent public health needs. Understanding regulatory approaches for approval of drugs for rare cancers and rare metabolic diseases could help meet the challenges of studying drugs for rare IFDs. A single-arm, controlled clinical trial with a high-quality external control(s), with confirmatory evidence from nonclinical studies, including pharmacokinetic/pharmacodynamic data in predictive animal models of the disease may support findings of effectiveness of new drugs and biologics. Control populations may include historical controls from published literature, patient registries, and/or contemporaneous external control groups. Continuous engagement among clinicians, industrial sponsors, and regulatory agencies to develop consensus on trial design and innovative development pathways for emergent and rare invasive fungal diseases is important.
A Multimodal Approach to Measuring Listening Effort: A Systematic Review on the Effects of Auditory Task Demand on Physiological Measures and Their Relationship
Authors: Keur-Huizinga Laura , Kramer Sophia E. , de Geus Eco J. C. , Zekveld Adriana A.
Published: June 2024

Objectives:

Listening effort involves the mental effort required to perceive an auditory stimulus, for example in noisy environments. Prolonged increased listening effort, for example due to impaired hearing ability, may increase risk of health complications. It is therefore important to identify valid and sensitive measures of listening effort. Physiological measures have been shown to be sensitive to auditory task demand manipulations and are considered to reflect changes in listening effort. Such measures include pupil dilation, alpha power, skin conductance level, and heart rate variability. The aim of the current systematic review was to provide an overview of studies to listening effort that used multiple physiological measures. The two main questions were: (1) what is the effect of changes in auditory task demand on simultaneously acquired physiological measures from various modalities? and (2) what is the relationship between the responses in these physiological measures?

Design:

Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, relevant articles were sought in PubMed, PsycInfo, and Web of Science and by examining the references of included articles. Search iterations with different combinations of psychophysiological measures were performed in conjunction with listening effort-related search terms. Quality was assessed using the Appraisal Tool for Cross-Sectional Studies.

Results:

A total of 297 articles were identified from three databases, of which 27 were included. One additional article was identified from reference lists. Of the total 28 included articles, 16 included an analysis regarding the relationship between the physiological measures. The overall quality of the included studies was reasonable.

Conclusions:

The included studies showed that most of the physiological measures either show no effect to auditory task demand manipulations or a consistent effect in the expected direction. For example, pupil dilation increased, pre-ejection period decreased, and skin conductance level increased with increasing auditory task demand. Most of the relationships between the responses of these physiological measures were nonsignificant or weak. The physiological measures varied in their sensitivity to auditory task demand manipulations. One of the identified knowledge gaps was that the included studies mostly used tasks with high-performance levels, resulting in an underrepresentation of the physiological changes at lower performance levels. This makes it difficult to capture how the physiological responses behave across the full psychometric curve. Our results support the Framework for Understanding Effortful Listening and the need for a multimodal approach to listening effort. We furthermore discuss focus points for future studies.
Spine Involvement and Vertebral Deformity in Patients Diagnosed with Chronic Recurrent Multifocal Osteomyelitis
Authors: Rogers Nathan D. , Trizno Anastasiya A. , Joyce Christopher D. , Roberts Jesse L. , Soep Jennifer B. , Donaldson Nathan J.
Published: June 2024

Background:

Chronic recurrent multifocal osteomyelitis (CRMO) is an inflammatory disorder of bone, typically arising adjacent to the physes of long bones but also seen throughout the skeleton. For patients with spinal involvement, CRMO lesions can cause compression deformities with a range of severity from minimal anterior wedging to circumferential height loss, known as vertebra plana. This study examines a large cohort of CRMO patients to determine the prevalence of spine involvement and vertebral deformity.

Methods:

This is a retrospective review of all patients with a diagnosis of CRMO seen at our institution between January 2003 and December 2020. These patients were identified through a prospectively maintained database of all CRMO patients seen at the institution. A retrospective review was undertaken to identify all patients with spinal involvement and determine the prevalence of CRMO in the spine and its effects on vertebral height and deformity.

Results:

Of 170 patients included in this study, 48 (28.2%) were found to have spinal involvement. Among patients with spinal involvement, vertebral body lesions were identified in 27 (56.3%) patients. The remaining lesions were in the sacrum or posterior elements. Radiographic evidence of the vertebral body height loss was noted in 23 of these 27 patients.

Conclusions:

This cohort of CRMO patients demonstrates that 28% of patients have spinal involvement, and 48% of those patients have vertebral body height loss. While the ideal treatment for spinal CRMO has yet to be determined, imaging studies, including whole-body MRI and spine-specific MRI, are useful in identifying vertebral lesions and deformities. Identification and surveillance of these lesions are important as the disorder has a relapsing and remitting course, and patients can develop significant vertebral body height loss. Once deformity has developed, we have seen no evidence of reconstitution of the height of the collapsed vertebra. Bisphosphonates have been successful in preventing the progression of vertebral body height loss.

Level of Evidence:

Level II: Retrospective study investigating spinal involvement and prevalence of vertebral body deformity in patients diagnosed with CRMO.
The Piggyback Superficial Circumflex Iliac Perforator Flap for Complex Free Flap Reconstructions
Authors: Yoshimatsu Hidehiko , Nakatsuka Kengo , Karakawa Ryo , Fuse Yuma , Yano Tomoyuki
Published: June 2024

This article introduces a reproducible strategy for complex reconstruction scenarios that require the use of two flaps. It specifically focuses on the utilization of the superficial circumflex iliac artery perforator (SCIP) flap as a secondary flap, particularly in complex cases where available arterial options are limited. In the first scenario, the SCIP flap is elevated simultaneously during elevation of a fibula bone flap. The pedicle of the fibula flap will be anastomosed to the recipient vessels, and the pedicle artery of the SCIP flap, the superficial circumflex iliac artery, will be anastomosed to the distal end of the peroneal artery. The SCIP flap pedicle offers greater length compared with a cutaneous flap sourced from the peroneal artery, thus providing increased flexibility for the flap inset. In the second scenario, the SCIP flap is combined with the anterolateral thigh (ALT) flap to manage a significant defect. The pedicle of the ALT flap is anastomosed to the recipient vessels, and the superficial circumflex iliac artery is anastomosed to the distal end of the pedicle artery of the ALT flap, the descending branch of the lateral circumflex femoral artery. The SCIP flap can be harvested simultaneously with a fibula flap or an ALT flap from the same side, and its arterial anastomosis can always be established with the distal ends of the arterial pedicle of these two flaps. This efficient and reproducible method can also contribute to minimal donor site morbidity and will be particularly valuable in settings where recipient artery choices are limited.
Point-of-care ultrasonography in acute kidney injury
Authors: Varanasi Paavana , Bhasin-Chhabra Bhavna , Koratala Abhilash
Published: June 2024

Point-of-care ultrasonography (POCUS) is emerging as a valuable tool in nephrology, providing real-time insights into the etiology of acute kidney injury (AKI). This narrative review explores POCUS applications in AKI, emphasizing its role in diagnostic kidney ultrasound and comprehensive hemodynamic assessments. AKI, prevalent in hospitalized patients, poses significant morbidity and mortality risks. POCUS aids in unraveling AKI’s multifaceted origins, categorizing it into hemodynamic, obstructive, and intrinsic renal causes. We discuss the utility of POCUS in urinary obstruction by identifying hydronephrosis and detecting stones and providing prompt diagnostic assistance. In intrinsic AKI, POCUS has limited utility but can potentially differentiate between acute and chronic kidney disease and identify infectious complications. POCUS-assisted hemodynamic AKI assessment involves thorough evaluation of the cardiac, lung, and end organ venous congestion. As technology advances, the role of POCUS in the diagnosis and management of AKI is likely to increase, offering a portable, cost-effective, and radiation-free bedside diagnostic modality. This also has the potential to improve patient outcomes. However, proper training in techniques of POCUS and an understanding of the limitations of POCUS are essential elements in ensuring its optimal and appropriate use in the right clinical context.
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

Introduction

Reconstruction 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.

Methods

A 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.

Results

Twenty-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.

Conclusions

Propeller 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

Background

Acellular 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.

Methods

A 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.

Results

A 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.

Conclusion

Low 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

Purpose: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

Virtual 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).

Significance

We 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

The 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.
Still waters run deep: Large scale genome rearrangements in the evolution of morphologically conservative Polyplacophora
Authors: Sigwart Julia D , Li Yunlong , Chen Zeyuan , Voncina Katarzyna , Sun Jin
Published: June 2024

Background: A major question in animal evolution is how genotypic and phenotypic changes are related, and whether ancient gene order is conserved in living clades. Chitons, the molluscan class Polyplacophora, retain a body plan and general morphology apparently little changed since the Palaeozoic. We present a comparative analysis of five reference quality genomes, including four de novo assemblies, covering all major chiton clades, and an updated phylogeny for the phylum. Results: We constructed 20 ancient molluscan linkage groups (MLGs) that are relatively conserved in bivalve karyotypes, but subject to re-ordering, rearrangement, fusion, or partial duplication among chitons, varying even between congeneric species. The largest number of novel fusions is in the most plesiomorphic clade Lepidopleurida, and the chitonid Liolophura japonica has a partial genome duplication, extending the occurrence of large-scale gene duplication within Mollusca. Conclusions: The extreme and dynamic genome rearrangements in this class stands in contrast to most other animals, demonstrating that chitons have overcome evolutionary constraints acting on other animal groups. The apparently conservative phenome of chitons belies rapid and extensive changes in genome.
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 Statement

Reliably 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

Flavonoids 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.
LAIR1 prevents excess inflammatory tissue damage inS. aureusskin infection and Cutaneous T-cell Lymphoma
Authors: Dorando Hannah K. , Mutic Evan C. , Tomaszewski Kelly L. , Tian Ling , Stefanov Mellisa K. , Quinn Chaz C. , Veis Deborah J. , Wardenburg Juliane Bubeck , Musiek Amy C. , Mehta-Shah Neha , Payton Jacqueline E.
Published: June 2024

Patients with cutaneous T cell lymphoma (CTCL) experience high morbidity and mortality due toS. aureusskin infections and sepsis, but the causative immune defect is unclear. We previously identified high levels of LAIR2, a decoy protein for the inhibitory receptor LAIR1, in advanced CTCL. Mice do not have a LAIR2 homolog, so we usedLair1knock-out (KO) mice to model LAIR2 overexpression. In a model of subcutaneousS. aureusskin infection,Lair1KO mice had significantly larger abscesses and areas of dermonecrosis compared to WT.Lair1KO exhibited a pattern of increased inflammatory responses in infection and sterile immune stimulation, including increased production of proinflammatory cytokines and myeloid chemokines, neutrophil ROS, and collagen/ECM remodeling pathways. Notably,Lair1KO infected skin had a similar bacterial burden and neutrophils and monocytes had equivalentS. aureusphagocytosis compared to WT. These findings support a model in which lack of LAIR1 signaling causes an excessive inflammatory response that does not improve infection control. CTCL skin lesions harbored similar patterns of increased expression in cytokine and collagen/ECM remodeling pathways, suggesting that high levels of LAIR2 in CTCL recapitulatesLair1KO, causing inflammatory tissue damage and compromising host defense againstS. aureusinfection.
NLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data
Authors: Chen Yunlu , Ruan Feng , Wang Ji-Ping
Published: June 2024

Spatial transcriptomics (ST) allows gene expression profiling within intact tissue samples but lacks single-cell resolution. This necessitates computational deconvolution methods to estimate the contributions of distinct cell types. This paper introduces NLSDeconv, a novel cell-type deconvolution method based on non-negative least squares, along with an accompanying Python package. Benchmarking against 18 existing deconvolution methods on various ST datasets demonstrates NLSDeconv’s competitive statistical performance and superior computational efficiency.

Availability and implementation

NLSDeconv is freely available with tutorial athttps://github.com/tinachentc/NLSDeconvas a Python package.
The Impact of Parabacteroides distasonis Colonization on Hosts' Microbiome, Metabolome, Immune Responses, and Diabetes Onset
Authors: Girdhar Khyati , Randall Audrey I , Dogru Yusuf Dogus , Howard Clarissa , Pezzella Alessandro , Henao Juan , Gautam Umesh Kumar , Ŝaŝinková Pavla , Hudcovic Tomáŝ , Schwarzer Martin , Kiebish Michael , ALTINDIS EMRAH
Published: June 2024

Type 1 Diabetes (T1D) is a chronic disease caused by autoimmune destruction of insulin-producing pancreatic β-cells. The insulin B-chain 9-23 (insB:9-23) peptide is established as a critical epitope in triggering T1D. In our previous study, we showed thatParabacteroides distasonis, a human gut commensal, contains an insB:9-23 mimic in its hprt protein (residues, 4-18). This mimic (hprt4-18) activates insB:9-23 specific T-cells, and colonization ofP. distasonisin female NOD mice enhanced diabetes onset. Additionally, the presence of hprt:4-18 sequence in the gut microbiome is associated with seropositivity in infants. However, the impact of the colonization on the gut microbiome and intestinal immune cell compositions, gut permeability, cytokine, and serum metabolome profiles were unknown. Here, we addressed this gap using specific pathogen-free (SPF) and germ-free (GF) NOD mouse models.P. distasoniscolonization had a minimal impact on gut microbiome composition and merely altered 28 ASVs upon colonization. In intraepithelial lymphocytes (IELs) ofP. distasoniscolonized SPF NOD mice, we observed a 1.72-fold reduction in T-helper cells and a 2.3-fold reduction in T- effector cells, along with a 1.85-fold reduction in B-cell populations. Further,P. distasonisdid not alter serum metabolome and cytokine levels except for a decrease in IL-15. We observed no difference in the gene expression related to gut permeability. Similar to SPF mice,P. distasoniscolonization in GF NOD mice induced severe insulitis without affecting gut permeability. On the other hand,P. distasonislysate could induce insB:9-23 specific T cells. Altogether, these findings demonstrate thatP. distasonisdoes not stimulate a nonspecific inflammatory immune response in the intestines, nor does it cause significant alterations in the gut microbiome, gut permeability, serum metabolome, or cytokine response. However, it does induce insulitis in GF NOD mice and activates insB:9-23 specific T-cells. These findings support our original hypothesis thatP. distasoniscolonization stimulates a specific immune response and enhances T1D onset in NOD mice via molecular mimicry.
THE CELLS ARE ALL-RIGHT: Regulation of theLeftygenes by separate enhancers in mouse embryonic stem cells
Authors: Taylor Tiegh , Zhu Hongyu Vicky , Moorthy Sakthi D. , Khader Nawrah , Mitchell Jennifer A.
Published: June 2024

Enhancers play a critical role in regulating precise gene expression patterns essential for development and cellular identity; however, how gene-enhancer specificity is encoded within the genome is not clearly defined. To investigate how this specificity arises within topologically associated domains (TAD), we performed allele-specific genome editing of sequences surrounding theLefty1andLefty2paralogs in mouse embryonic stem cells. TheLeftygenes arose from a tandem duplication event and these genes interact with each other in chromosome conformation capture assays which place these genes within the same TAD. Despite their physical proximity, we demonstrate that these genes are primarily regulated by separate enhancer elements. Through CRISPR-Cas9 mediated deletions to remove the intervening chromatin between theLeftygenes, we reveal a distance-dependent dosage effect of theLefty2enhancer onLefty1expression. These findings indicate a potential role for both discrete CTCF bound regions of the genome and chromatin distance in insulating gene expression domains in theLeftylocus in the absence of architectural insulation.
Advancing source tracking: systematic review and source-specific genome database curation of fecally shed prokaryotes
Authors: Lindner Blake G. , Choudhury Rakin A. , Pinamang Princess , Bingham Lilia , D’Amico Isabelle , Hatt Janet K. , Konstantinidis Konstantinos T. , Graham Katherine E.
Published: June 2024

Approaches for shotgun metagenomic sequencing are being adapted to many environmental monitoring tasks but remain poorly suited for source attribution within fecal source tracking (FST) studies due to a lack of knowledge regarding the source specificity of fecally shed microbial populations. To address this gap, we performed a systematic literature review and curated a large collection of genomes (n=26,018) representing fecally shed prokaryotic species across broad and narrow source categories commonly implicated in FST studies of recreational waters (i.e., cats, dogs, cows, seagulls, chickens, pigs, birds, ruminants, human feces, and wastewater). These data include genome sequences recovered from metagenomic and isolation-based studies which we examined extensively with comparative genomic approaches to characterize trends across source categories and produce a finalized genome database for each source category which is available online (n=12,730). We find that across these sources, the total number of genomes recovered varies substantially: from none in seagulls to 9,085 in pigs.

According to available data, on average 81% of the genomes representing species-level populations occur only within a single source. Using fecal slurries to test the performance of each source database, we report read capture rates that vary with fecal source alpha diversity and database size. Lastly, while extensive work has been performed on the rumen system of cows and other ruminants, we note the scarcity of genomic characterization of prokaryotes in the feces of these animals. We expect this resource to be useful to FST-related objectives, One Health research, and sanitation efforts globally.

Table of Contents Graphical Abstract

Synopsis

We curate nine prokaryotic genomic databases for fecal source-tracking, summarize their source-specificity, and show their usefulness by bioinformatically testing mock impaired surface water samples.
Cancer Cachexia in STK11/LKB1-mutated NSCLC is Dependent on Tumor-secreted GDF15
Authors: Yu Jinhai , Guo Tong , Gupta Arun , Llano Ernesto M. , Wajahat Naureen , Slater Sean , Deng Qing , Akbay Esra A. , Shelton John M. , Evers Bret M. , Wu Zhidan , Tzameli Iphigenia , Pashos Evanthia , Minna John D. , Iyengar Puneeth , Infante Rodney E.
Published: June 2024

Cachexia is a wasting syndrome comprised of adipose, muscle, and weight loss observed in cancer patients. Tumor loss-of-function mutations inSTK11/LKB1, a regulator of the energy sensor AMP-activated protein kinase, induce cancer cachexia (CC) in preclinical models and are associated with cancer-related weight loss in NSCLC patients. Here we characterized the relevance of the NSCLC-associated cachexia factor growth differentiation factor 15 (GDF15) in several patient-derived and genetically engineeredSTK11/LKB1-mutant NSCLC cachexia lines. Both tumor mRNA expression and serum concentrations of tumor-derived GDF15 were significantly elevated in multiple mice transplanted with patient-derivedSTK11/LKB1-mutated NSCLC lines. GDF15 neutralizing antibody administered to mice transplanted with patient- or mouse-derivedSTK11/LKB1-mutated NSCLC lines suppressed cachexia-associated adipose loss, muscle atrophy, and changes in body weight. The silencing ofGDF15in multiple human NSCLC lines was also sufficient to eliminatein vivocirculating GDF15 levels and abrogate cachexia induction, suggesting that tumor and not host tissues represent a key source of GDF15 production in these cancer models. Finally, reconstitution of wild-typeSTK11/LKB1in a humanSTK11/LKB1loss-of-function NSCLC line that normally induces cachexiain vivocorrelated with the absence of tumor-secreted GDF15 and rescue from the cachexia phenotype. The current data provide evidence for tumor-secreted GDF15 as a conduit and a therapeutic target through which NSCLCs withSTK11/LKB1loss-of-function mutations promote cachexia-associated wasting.