bluuebunny/crossref_metadata_2025_split huggingface dataset:
Postoperative neurological symptoms following arthroscopic shoulder surgery with interscalene block: an exploratory secondary analysis of pooled randomized controlled trial data
Authors: Frost Samantha , Rodrigues Daniel , Amadeo Ryan J J , Wolfe Scott , Funk Faylene , Ferguson Celeste , Brown Holly , MacDonald Peter , Dufault Brenden , Mutter Thomas Charles 
Published: June 2023

ObjectivePostoperative neurological symptoms (PONS) are recognized complications of regional anesthesia and orthopedic surgery. We aimed to better characterize prevalence and potential risk factors in a homogeneous population of randomized, controlled trial participants.MethodsData were pooled from two randomized controlled trials of analgesia after interscalene block with perineural or intravenous adjuvants (NCT02426736,NCT03270033). Participants were at least 18 years of age and undergoing arthroscopic shoulder surgery at a single ambulatory surgical center. PONS were assessed by telephone follow-up at 14 days and 6 months postoperatively, and defined as patient report of numbness, weakness, or tingling in the surgical limb, alone or in combination, and regardless of severity or etiology.ResultsAt 14 days, PONS occurred in 83 of 477 patients (17.4%). Among these 83 patients, 10 (12.0%) continued to have symptoms a half-year after surgery. In exploratory univariate analyses, no patient, surgical or anesthetic characteristics were significantly associated with 14-day PONS except for lower postoperative day 1 Quality of Recovery-15 questionnaire total score (OR 0.97 (95% CI, 0.96 to 0.99), p<0.01). This result was driven largely by the emotional domain question scores (OR 0.90 95% CI 0.85 to 0.96, p<0.001). Report of all three of numbness, weakness and tingling at 14 days vs other 14-day symptom combinations was associated with persistent PONS at 6 months (OR 11.5 95% CI 2.2 to 61.8, p<0.01).ConclusionPONS are common after arthroscopic shoulder surgery performed with single injection ultrasound-guided interscalene blocks. No definitive mitigating risk factors were identified.
Equal mixture of 2% lidocaine with adrenaline and 0.5% bupivacaine 20 mL provided faster onset of complete conduction blockade during ultrasound-guided supraclavicular brachial plexus block than 20 mL of 0.5% bupivacaine alone: a randomized double-blinded clinical trial
Authors: R Sripriya , T Sivashanmugam , Rajadurai Daniel , Parthasarathy S 
Published: June 2023

IntroductionRecent evidence has questioned the advantage of local anesthetic (LA) combinations. This study tested the hypothesis that mixing rapid-onset (lidocaine) and long-duration (bupivacaine) LA would provide faster onset of complete conduction blockade (CCB) compared with bupivacaine alone and longer duration of analgesia compared with lidocaine alone during low-volume (20 mL) ultrasound-guided (USG) supraclavicular brachial plexus block (SCBPB).MethodsSixty-three patients receiving USG-SCBPB were randomly allocated into: groupL: 20 mL 2% lidocaine with epinephrine 1:200 000;group B:20 mL 0.5% bupivacaine;group LB: 20 mL of equi-volume mixture of both drugs. Sensory and motor blockade was recorded on a three point sensory and motor assessment scale at 10 min intervals for up to 40 min and the total composite score (TCS) at each time point was determined. The duration of analgesia was also noted.ResultsThe mean time to CCB of group LB (16±7 min) was comparable (p>0.05) with group L (14±6 min) and group B (21±8 min) in patients who were attained CCB. However, the proportion of patients attaining complete conduction block (TCS=16/16) was significantly lower (p=0.0001) in group B (48%) when compared with group L (95%) and group LB (95%) at the end of 40 min. The median (IQR) duration of postoperative analgesia was longest in group B; 12.2 (12–14.5) hours, followed by group LB 8.3 (7–11) hours and 4 (2.7–4.5) hours in group L.ConclusionAt 20 mL LA volume, equal mixture of lidocaine and bupivacaine provided significantly faster onset of CCB compared with bupivacaine alone and longer duration of postoperative analgesia compared with lidocaine alone but shorter than bupivacaine alone during low-volume USG-SCBPB.Trial registration numberCTRI/2020/11/029359.
Lorentz group equivariant autoencoders
Authors: Hao Zichun , Kansal Raghav , Duarte Javier , Chernyavskaya Nadezda 
Published: June 2023

AbstractThere has been significant work recently in developing machine learning (ML) models in high energy physics (HEP) for tasks such as classification, simulation, and anomaly detection. Often these models are adapted from those designed for datasets in computer vision or natural language processing, which lack inductive biases suited to HEP data, such as equivariance to its inherent symmetries. Such biases have been shown to make models more performant and interpretable, and reduce the amount of training data needed. To that end, we develop the Lorentz group autoencoder (LGAE), an autoencoder model equivariant with respect to the proper, orthochronous Lorentz group $$\textrm{SO}^+(3,1)$$

SO
+

(
3
,
1
)

, with a latent space living in the representations of the group. We present our architecture and several experimental results on jets at the LHC and find it outperforms graph and convolutional neural network baseline models on several compression, reconstruction, and anomaly detection metrics. We also demonstrate the advantage of such an equivariant model in analyzing the latent space of the autoencoder, which can improve the explainability of potential anomalies discovered by such ML models.
Astrophysical implications of an eternal homogeneous gravitational collapse model with a parametrization of expansion scalar
Authors: Jaiswal Annu , Kumar Rajesh , Srivastava Sudhir Kumar , Pacif S. K. J. 
Published: June 2023

AbstractIn this study, we continue our previous work (Annu et al. 2023) by introducing a novel parametrization of the expansion scalar $$\Theta $$
Θ
as a rational function of time t. The paper provides a comprehensive analysis of a homogeneous gravitational collapsing system, wherein the exact solutions of the Einstein field equations (EFEs) are determined using a new parametrization of $$\Theta $$
Θ
in a model-independent way. The model is especially significant for the astrophysical applications because we have addressed the physical and geometrical quantities of the model in terms of Schwarzschild mass M. We have estimated the numerical value of the model parameter involved in the functional form of $$\Theta $$
Θ
-parametrization using the masses and radii data of some massive stars namely, Westerhout 49-2, BAT99-98, R136a1, R136a2, WR 24, Pismis 24-1, $$\lambda $$
λ
Cephei, $$\alpha $$
α
Camelopardalis, $$\beta $$
β
Canis Majoris. We have presented theoretical investigations about such astrophysical stellar systems. The formation of an apparent horizon is also studied for the collapsing system, and it has been shown that our model produces a continuing collapsing scenario of star (an eternal collapsing object).
Crossover for Cardinality Constrained Optimization
Authors: Friedrich Tobias , Kötzing Timo , Radhakrishnan Aishwarya , Schiller Leon , Schirneck Martin , Tennigkeit Georg , Wietheger Simon 
Published: June 2023

To understand better how and why crossover can benefit constrained optimization, we consider pseudo-Boolean functions with an upper bound
B
on the number of 1-bits allowed in the length-
n
bit string (i.e., a cardinality constraint). We investigate the natural translation of the OneMax test function to this setting, a linear function where
B
bits have a weight of 1+ 1/
n
and the remaining bits have a weight of 1. Friedrich et al. [TCS 2020] gave a bound of Θ (
n
2
) for the expected running time of the (1+1) EA on this function.

Part of the difficulty when optimizing this problem lies in having to improve individuals meeting the cardinality constraint by flipping a 1 and a 0 simultaneously. The experimental literature proposes balanced operators, preserving the number of 1-bits, as a remedy. We show that a balanced mutation operator optimizes the problem in
O(n
log
n
) if
n-B
=
O
(1). However, if
n-B
= Θ (
n
), we show a bound of Ω (
n
2
), just as for classic bit mutation. Crossover together with a simple island model gives running times of
O
(
n
2
/ log
n
) (uniform crossover) and

\(O(n\sqrt {n})\)

(3-ary majority vote crossover). For balanced uniform crossover with Hamming-distance maximization for diversity, we show a bound of
O
(
n
log
n
).

As an additional contribution, we present an extensive analysis of different balanced crossover operators from the literature.
Comparison of Modified Manual Acid-Phenol Chloroform Method and Commercial RNA Extraction Kits for Resource Limited Laboratories
Authors: Sakyi Samuel Asamoah , Effah Alfred , Naturinda Emmanuel , Senu Ebenezer , Opoku Stephen , Amoani Benjamin , Agordzo Samuel Kekeli , Mensah Oscar Simon Olympio , Grant James , Abban Elizabeth , Buckman Tonnies Abeku , Kwarteng Alexander , Ephraim Richard K. Dadzie , Danquah Kwabena Owusu 
Published: June 2023

Background and Aim. RNA extraction is a commonly used technique in molecular biology. In recent years, commercially available RNA extraction kits have largely replaced conventional approaches. However, these commercial kits are expensive and are not readily available in many resource-constrained institutions and laboratories. This study therefore compared the performance of the conventional acid guanidinium thiocyanate-phenol-chloroform (AGPC) extraction method to QIAamp® Viral RNA Mini Kit (QIAGEN, Cat. No. 52906) and OxGEn RNA Kit (OxGEn Molecular Solutions, GE-009) to build an in-house RNA extraction technique from blood and oral swab samples. Method. In a comparative experimental cross-sectional study, RNA was extracted from oral swabs and blood samples from 25 healthy individuals at the Department of Molecular Medicine, KNUST. RNA was extracted by the manual AGPC extraction method and commercial RNA extraction kits. The quantity (ng/μl) and purities (260/280 nm) of the extracted RNA were measured spectrophotometrically using the IMPLEN NanoPhotometer® N60. The presence of RNA in the extracts was confirmed using 2% agarose gel electrophoresis. Statistical analyses were conducted using R language. Results. The yield of RNA extracted from blood and oral swab samples using modified AGPC was significantly higher compared to the commercial methods (

p

< 0.0001). However, the purity of RNA extracted by the manual AGPC method from blood was significantly lower than the commercial methods (

p

< 0.0001). Moreover, the purity from oral swabs using the manual AGPC method was significantly lower compared to QIAamp (

p

< 0.0001) and the OxGEn kits method (

p

< 0.001). Conclusion. The modified manual AGPC method has a very high yield of RNA extracts using blood samples, which could serve as an alternate cost-effective method for RNA extraction in resource-limited laboratories; however, its purity may not be suitable for downstream processes. Moreover, the manual AGPC method may not be suitable for extracting RNA from oral swab samples. Future investigation is needed to improve the purity of the manual AGPC RNA extraction method and also confirmation of the obtained results by PCR amplification and RNA purity verification by sequencing.
Elevated EVL Methylation Level in the Normal Colon Mucosa Is a Potential Risk Biomarker for Developing Recurrent Adenomas
Authors: Yu Ming , Carter Kelly T. , Baker Kelsey K. , Redman Mary W. , Wang Ting , Vickers Kathy , Li Christopher I. , Cohen Stacey A. , Krane Mukta , Ose Jennifer , Gigic Biljana , Figueiredo Jane C. , Toriola Adetunji T. , Siegel Erin M. , Shibata David , Schneider Martin , Ulrich Cornelia M. , Dzubinski Lynda A. , Schoen Robert E. , Grady William M. 
Published: June 2023

Abstract

Background:
Individuals with adenomatous colorectal polyps undergo repeated colonoscopy surveillance to identify and remove metachronous adenomas. However, many patients with adenomas do not develop recurrent adenomas. Better methods to evaluate who benefits from increased surveillance are needed. We evaluated the use of altered EVL methylation as a potential biomarker for risk of recurrent adenomas.

Methods:
Patients with ≥1 colonoscopy had EVL methylation (mEVL) measured with an ultra-accurate methylation-specific droplet digital PCR assay on normal colon mucosa. The association between EVL methylation levels and adenoma or colorectal cancer was evaluated using three case/control definitions in three models: unadjusted (model 1), adjusting for baseline characteristics (model 2), and an adjusted model excluding patients with colorectal cancer at baseline (model 3).

Results:
Between 2001 and 2020, 136 patients were included; 74 healthy patients and 62 patients with a history of colorectal cancer. Older age, never smoking, and baseline colorectal cancer were associated with higher levels of mEVL (P ≤ 0.05). Each log base 10 difference in mEVL was associated with an increased risk of adenoma(s) or cancer at/after baseline for model 1 [OR, 2.64; 95% confidence interval (CI), 1.09–6.36], and adenoma(s) or cancer after baseline for models 1 (OR, 2.01; 95% CI, 1.04–3.90) and model 2 (OR, 3.17; 95% CI, 1.30–7.72).

Conclusions:
Our results suggest that EVL methylation level detected in the normal colon mucosa has the potential to be a biomarker for monitoring the risk for recurrent adenomas.

Impact:
These findings support the potential utility of EVL methylation for improving the accuracy for assigning risk for recurrent colorectal adenomas and cancer.
Abstract 1027: Assessment of tumor mutation burden (TMB) based on whole exome sequencing using extracellular vesicles-derived DNA obtained from bronchoalveolar lavage fluid (BALF) in advanced NSCLC patients treated with pembrolizumab
Authors: Kim Heejoung , Hur Jaeyoung , Kim Wan Seop , Kim In Ae , Park Dong Il , Oh In-Jae , Lee Kye Young 
Published: June 2023

Abstract
Background: Although multiple immune checkpoint inhibitors showed improved outcomes in patients with high tumor mutational burden (TMB) as well as high PD-L1 expression, obtaining adequate tumor tissue for various molecular testing including next-generation sequencing (NGS) is not a simple issue in patients with advanced non-small cell lung cancer (NSCLC). We aimed to assess TMB based on whole exome sequencing (WES) using extracellular vesicles (EV)-derived DNA isolated from bronchoalveolar lavage fluid (BALF) and determine the correlation of TMB between BALF and tissue.
Methods: Patients diagnosed with advanced NSCLC and who were treated with pembrolizumab between December 2018 and December 2021 were included in this multicenter translational cohort study. The correlation of TMB between BALF and tissue measured by WES was evaluated by Spearman’s rank correlation coefficient in matched BALF and tissue samples from 62 patients. We analyzed the association of BALF TMB level with progression-free survival (PFS) and response to pembrolizumab.
Results: Of 62 patients, 47 (75.8%) had evaluable tissue TMB and 57 (91.9%) had evaluable BALF TMB. There were no significant differences between BALF and tissue with regards to DNA amounts, estimated library size, mean depth, and uniformity. Median tissue TMB and BALF TMB were 6.02 and 2.16 mut/Mb, respectively. There was a weak positive correlation between tissue TMB and BALF TMB (r=0.23, p &lt; 0.001), whereas BALF TMB found higher correlations with tissue TMB in patients with squamous cell carcinoma (r=0.77, p &lt; 0.001). Neither tissue TMB nor BALF TMB showed significant differences PFS or ORR benefit for treatment with pembrolizumab, however the BALF TMB of patients who had been treated with pembrolizumab for more than 6 months was higher than that of those who did not (p=0.039).
Conclusions: The findings suggest that NGS using BALF EV DNA is feasible for TMB calculation to overcome the matter of small biopsy issue in advanced NSCLC patients, which may play a supplementary serve as a potential biomarker of clinical benefit in patients with NSCLC treated with pembrolizumab.
Citation Format: Heejoung Kim, Jaeyoung Hur, Wan Seop Kim, In Ae Kim, Dong Il Park, In-Jae Oh, Kye Young Lee. Assessment of tumor mutation burden (TMB) based on whole exome sequencing using extracellular vesicles-derived DNA obtained from bronchoalveolar lavage fluid (BALF) in advanced NSCLC patients treated with pembrolizumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1027.
Abstract 106: Intratumoral heterogeneity of glioblastoma is attributed to precancerous cells derived from neural stem cells
Authors: Lee Jeong Ho , Kim Hyun Jung , Kang Seok-Gu 
Published: June 2023

Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain cancer in adults. We and other groups have identified mutation-harboring neural stem cells (NSCs) in the subventricular zone (SVZ) as cells-of-origin carrying driver mutations (Lee et al, Nature 2018). However, little is known about the evolutional process by which mutation-harboring NSCs in the SVZ transform into distant cancer cells with a high degree of molecular heterogeneity. Here, using a spontaneous, somatic mouse model that recapitulates human GBM arising from NSCs that carry driver mutations, we show that mutation-harboring NSCs transform into precancerous cells through oligodendrocyte progenitor cell (OPC) lineage specification during tumor evolution. These precancerous cells show dysregulated translation and/or modification of extracellular matrix (ECM) prior to tumor formation. They subsequently give rise to GBMs with intratumoral heterogeneity exhibiting multiple developmental cell states as in human GBM, and also show activation of additional transcriptional programs, including immune evasion, ECM remodeling, epithelial-mesenchymal transition, and proliferation. Importantly, we further identified precancerous cell populations carrying driver mutations, namely gain of chromosome 7 and loss of chromosome 10 in tumor-free SVZ tissues from GBM patients with intratumoral heterogeneity. These human precancerous cells indeed exhibited OPC and neural progenitor cell-like expression patterns similar to those in our spontaneous GBM mouse model. Thus, our results demonstrate that cell-type specification of precancerous cells with oncogenic transcriptional programs underlie evolution of GBM from mutation-harboring NSCs and intratumoral heterogeneity.
Citation Format: Jeong Ho Lee, Hyun Jung Kim, Seok-Gu Kang. Intratumoral heterogeneity of glioblastoma is attributed to precancerous cells derived from neural stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 106.
Abstract 1198: T cell receptor (TCR) landscape of childhood brain tumors
Authors: Raphael Itay , Nisnboym Michal , Raphael Rebecca A. , Uttam Shikhar , Pollack Ian F. , Chikina Maria , Rajasundaram Dhivyaa , Kohanbash Gary 
Published: June 2023

Abstract
T lymphocytes have a unique ability to recognize a vast array of antigens prompt by an enormous T cell receptor (TCR) repertoire. Characterization of tumor-infiltrating T cells (TILs) is key to understand MHC-restricted anti-tumor immunity and for developing T cell-centered immunotherapies such as adoptive cell therapy and tumor vaccines. In the current work, we investigated RNA-Seq data from 997 pediatric brain tumor patients and performed a large-scale comprehensive examination of the immunogenomic and TCR landscape of TILs across the entire spectrum of pediatric brain tumors. We show that the relative ratio between T cell clonal diversity and T cell abundance within each sample, represented by the clonal expansion index (CEI), is a strong predictor of prognosis both within and between tumor types. Interestingly, we show that CEI is strongly associated with molecular subgroups of medulloblastoma but not with known genomic features of these subgroups. Investigation of TCR clonotypes recognizing a common recurrent tumor-antigen across patients based on CDR3 homology and characteristics, reveals 9 TCR clusters which are tumor-type restricted with defined prognoses and HLA dominance. Using computational immunogenomics and machine learning-based investigations of these clusters we identified novel putative HLA-restricted tumor antigens which could bind and activate the clusters’ specific TCRs. Importantly, our framework grounded the foundations for developing a precision medicine approach of T cell-centered immunotherapies. These findings have major implications for understanding the interplay between T cell and tumor genomics, and for developing new immunotherapies for children with brain tumors and other cancers.
Citation Format: Itay Raphael, Michal Nisnboym, Rebecca A. Raphael, Shikhar Uttam, Ian F. Pollack, Maria Chikina, Dhivyaa Rajasundaram, Gary Kohanbash. T cell receptor (TCR) landscape of childhood brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1198.