bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rituximab Chimeric Anti-CD20 Monoclonal Antibody Therapy for Relapsed Indolent Lymphoma: Half of Patients Respond to a Four-Dose Treatment Program
Authors: McLaughlin P , Grillo-López A J , Link B K , Levy R , Czuczman M S , Williams M E , Heyman M R , Bence-Bruckler I , White C A , Cabanillas F , Jain V , Ho A D , Lister J , Wey K , Shen D , Dallaire B K 
Published: January 2023

PURPOSE The CD20 antigen is expressed on more than 90% of B-cell lymphomas. It is appealing for targeted therapy, because it does not shed or modulate. A chimeric monoclonal antibody more effectively mediates host effector functions and is itself less immunogenic than are murine antibodies. PATIENTS AND METHODS This was a multiinstitutional trial of the chimeric anti-CD20 antibody, IDEC-C2B8. Patients with relapsed low grade or follicular lymphoma received an outpatient treatment course of IDEC-C2B8 375 mg/m2 intravenously weekly for four doses. RESULTS From 31 centers, 166 patients were entered. Of this intent-to-treat group, 48% responded. With a median follow-up duration of 11.8 months, the projected median time to progression for responders is 13.0 months. Serum antibody levels were sustained longer after the fourth infusion than after the first, and were higher in responders and in patients with lower tumor burden. The majority of adverse events occurred during the first infusion and were grade 1 or 2; fever and chills were the most common events. Only 12% of patients had grade 3 and 3% grade 4 toxicities. A human antichimeric antibody was detected in only one patient. CONCLUSION The response rate of 48% with IDEC-C2B8 is comparable to results with single-agent cytotoxic chemotherapy. Toxicity was mild. Attention needs to be paid to the rate of antibody infusion, with titration according to toxicity. Further investigation of this agent is warranted, including its use in conjunction with standard chemotherapy.
Mismatch Repair and Microsatellite Instability Testing for Immune Checkpoint Inhibitor Therapy: ASCO Endorsement of College of American Pathologists Guideline
Authors: Vikas Praveen , Messersmith Hans , Compton Carolyn , Sholl Lynette , Broaddus Russell R. , Davis Anjee , Estevez-Diz Maria , Garje Rohan , Konstantinopoulos Panagiotis A. , Leiser Aliza , Mills Anne M. , Norquist Barbara , Overman Michael J. , Sohal Davendra , Turkington Richard C. , Johnson Tyler 
Published: January 2023

PURPOSE The College of American Pathologists (CAP) has developed a guideline on testing for mismatch repair (MMR) and microsatellite instability (MSI) for patients considered for immune checkpoint inhibitor therapy. ASCO has a policy and set of procedures for endorsing clinical practice guidelines that have been developed by other professional organizations. METHODS The CAP guideline was reviewed for developmental rigor by methodologists. An ASCO Endorsement Panel subsequently reviewed the content and the recommendations. RESULTS The ASCO Endorsement Panel determined that the recommendations from the CAP guideline, published on August 3, 2022, are clear, thorough, and based on the most relevant scientific evidence. ASCO endorses Mismatch Repair and Microsatellite Instability Testing for Immune Checkpoint Inhibitor Therapy: Guideline From the College of American Pathologists in Collaboration With the Association for Molecular Pathology and Fight Colorectal Cancer. RECOMMENDATIONS Within the guideline, MMR immunohistochemistry (IHC), MSI polymerase chain reaction, and MSI next-generation sequencing are all recommended testing options for colorectal cancer, MMR-IHC and MSI-polymerase chain reaction for gastroesophageal and small bowel cancer, and only MMR-IHC for endometrial cancer. No recommendation in favor of any testing method over another could be made for any other cancer. Tumor mutational burden was not recommended as a surrogate for DNA MMR deficiency. If MMR deficiency consistent with Lynch syndrome is detected, it should be communicated to the treating physician. Additional information is available at www.asco.org/molecular-testing-and-biomarkers-guidelines .
STK11Inactivation Predicts Rapid Recurrence in Inoperable Early-Stage Non–Small-Cell Lung Cancer
Authors: Katipally Rohan R. , Spurr Liam F. , Gutiontov Stanley I. , Turchan William Tyler , Connell Philip , Juloori Aditya , Malik Renuka , Binkley Michael S. , Jiang Alice L. , Rouhani Sherin J. , Chervin Carolina Soto , Wanjari Pankhuri , Segal Jeremy P. , Ng Victor , Loo Billy W. , Gomez Daniel R. , Bestvina Christine M. , Vokes Everett E. , Ferguson Mark K. , Donington Jessica S. , Diehn Maximilian , Pitroda Sean P. 
Published: January 2023

PURPOSEMolecular factors predicting relapse in early-stage non–small-cell lung cancer (ES-NSCLC) are poorly understood, especially in inoperable patients receiving radiotherapy (RT). In this study, we compared the genomic profiles of inoperable and operable ES-NSCLC.MATERIALS AND METHODSThis retrospective study included 53 patients with nonsquamous ES-NSCLC (stage I-II) treated at a single institution (University of Chicago) with surgery (ie, operable; n = 30) or RT (ie, inoperable; n = 23) who underwent tumor genomic profiling. A second cohort of ES-NSCLC treated with RT (Stanford, n = 39) was included to power clinical analyses. Prognostic gene alterations were identified and correlated with clinical variables. The primary clinical end point was the correlation of prognostic genes with the cumulative incidence of relapse, disease-free survival, and overall survival (OS) in a pooled RT cohort from the two institutions (N = 62).RESULTSAlthough the surgery cohort exhibited lower rates of relapse, the RT cohort was highly enriched for somatic STK11 mutations (43% v 6.7%). Receiving supplemental oxygen (odds ratio [OR] = 5.5), 20+ pack-years of tobacco smoking (OR = 6.1), and Black race (OR = 4.3) were associated with increased frequency of STK11 mutations. In the pooled RT cohort (N = 62), STK11 mutation was strongly associated with inferior oncologic outcomes: 2-year incidence of relapse was 62% versus 20% and 2-year OS was 52% versus 85%, remaining independently prognostic on multivariable analyses (relapse: subdistribution hazard ratio = 4.0, P = .0041; disease-free survival: hazard ratio, 6.8, P = .0002; OS: hazard ratio, 6.0, P = .022). STK11 mutations were predominantly associated with distant failure, rather than local.CONCLUSIONIn this cohort of ES-NSCLC, STK11 inactivation was associated with poor oncologic outcomes after RT and demonstrated a novel association with clinical hypoxia, which may underlie its correlation with medical inoperability. Further validation in larger cohorts and investigation of effective adjuvant systemic therapies may be warranted.
Lsp1 partially substitutes for Pil1 function in eisosome assembly under stress conditions
Authors: Vesela Petra , Zahumensky Jakub , Malinsky Jan 
Published: January 2023

ABSTRACT
Eisosomes are large hemitubular structures that underlie the invaginated microdomains in the plasma membrane of various ascomycetous fungi, lichens and unicellular algae. In fungi, they are organized by BAR-domain containing proteins of the Pil1 family. Two such proteins, Pil1 and Lsp1, participate in eisosome formation in the yeast Saccharomyces cerevisiae. Under normal laboratory conditions, deletion of the PIL1 gene results in the inability of cells to assemble wild-type-like eisosomes. We found that under certain stress conditions, Lsp1 partially substitutes for the Pil1 function and mediates assembly of eisosomes, specifically following a decrease in the activity of serine palmitoyltransferase, for example, in response to hyperosmotic stress. Besides Lsp1, the assembly of eisosomes lacking Pil1 also requires Seg1 and Nce102 proteins. Using next-generation sequencing, we found that the seg1Δnce102Δpil1Δ strain, which is unable to form eisosomes, overexpresses genes coding for proteins of oxidative phosphorylation and tricarboxylic acid cycle. By contrast, genes involved in DNA repair, ribosome biogenesis and cell cycle are downregulated. Our results identify Lsp1 as a stress-responsive eisosome organizer and indicate several novel functional connections between the eisosome and essential cellular processes.
Antioxidant and phytometabolite profiles of ethanolic extract from the cascara pulp of Coffea arabica collected from Gayo Highland: A study for potential photoaging agent
Authors: Lestari Wahyu , Hasballah Kartini , Listiawan M. Yulianto , Sofia Sofia 
Published: January 2023

Background: As the most abundant coffee by-product, cascara pulp has been considered a good source of antioxidants which could be used to prevent photoaging. The aim of this study was to determine the phytometabolite profiles, antioxidant and photoaging properties of the ethanolic extract of Coffea arabica cascara pulp. Methods: Ethanolic maceration was performed on the fine powder of C. arabica cascara pulp collected from Gayo Highland, Aceh Province, Indonesia. The filtrate obtained was evaluated for its 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, total phenolic content (TPC), and total flavonoid content (TFC). The phytometabolite profiling was conducted qualitatively using reagents and quantitatively using gas chromatography—mass spectroscopy (GC-MS). The potential of the cascara pulp phytometabolites in inhibiting activator protein-1 (AP-1) was evaluated through molecular docking. Results: The extract had TPC and TFC of 2.04 mg gallic acid equivalent/g extract and 91.81 mg quercetin equivalent/g extract, respectively. The half-maximal inhibitory concentration (IC50) for the DPPH inhibition reached as low as 9.59 mg/L. Qualitative phytocompound screening revealed the presence of alkaloids, saponins, tannins, flavonoids, steroids, quinones, polyphenols, and triterpenoids. GC-MS revealed the extract containing 5-hydroxy-methylfurfural (22.31%); 2,5 dimethyl 4 hidroxy 3(2H) furanone (0.74%); and caffeine (21.07%), which could form interaction with AP-1 with binding energies of -172.8, -150.8, and -63.188 kJ/mol, respectively. Conclusion: Ethanolic extract from C. arabica cascara pulp potentially have anti-photoaging properties which is worthy for further investigations in the future.
Genetic mapping and pedigree analysis of non-syndromic congenital deafness in Surabaya, Indonesia
Authors: Purnami Nyilo , Kusumagani Hamam , Nugroho Puguh Setyo , Faizah Zakiyatul , Moon In Seok 
Published: January 2023

Background: Genetic mutations cause 50-75% of congenital deafness. Congenital deafness is a disease divided into syndromic and non-syndromic types. Type B special schools facilitate children with deafness in Surabaya. This study aimed to identify a mutation gene that causes non-syndromic hearing impairment in school students. Methods: This research was an analytic observational study using a cross-sectional method applying simple random sampling of non-syndromic deaf children. The applied tests were pure tone audiometry, polymerase chain reaction (PCR), and hybridization tests. Subjects were evaluated on the pedigree route and then analyzed. Results: A total of 138 participants with non-syndromic hearing loss were enrolled in this study and 49 patients met the inclusion criteria. The subject’s average age was 16.16 years, with more male subjects than female. The hybridization results obtained six genetic mutations, one subject with mtDNA 1555, one subject with GJB2-299, two subjects with SLC26A4-IVS(7)2, and 3 subjects with unknown mutations. In pedigree analysis, the same genetic mutation was found in two generations of subjects with mtDNA 1555 and GJB2-299 mutations, and mutations of more than one genetic type were found in two generations of subjects with the SLC26A4-IVS(7)2 mutation. Conclusions: This study obtained six genetic mutations in non-syndromic congenital deaf children. Non-syndromic congenital deafness in Indonesia was found to have genetic mutations as a health risk. The risk was heredity with diverse inheritance patterns.
Pre-clinical undergraduate students’ perspectives on the adoption of virtual and augmented reality to their dental learning experience: A one-group pre- and post-test design protocol
Authors: Afrashtehfar Kelvin I. , Yang Jing-Wen , Al-Sammarraie A. , Chen Hui , Saeed Musab H. 
Published: January 2023

Background: We live in a time where traditional education has rapidly incorporated online modalities due to the recent SARS-CoV-2 (COVID-19) safety measures such as social distancing. Regardless of these challenges, health education constantly strives to implement the best technologies available for an effective student deep learning outcome. Virtual (VR) and augmented reality (AR) in the dental pre-clinical stage may help stimulate students to better understand the foundation material prescribed in the curriculum. Most visual material available for students is still mainly based on 2D graphics. Thus, this study will attempt to evaluate the students' perceptions about implementing VR/AR technologies in the learning setting. Methods: A single-group pretest-posttest design will be implemented where students will be exposed to VR/AR and fill out two questionnaires, one before and one after the exposure. Conclusions: This project is intended to start once the institutional ethical approval is obtained. It is expected that the analysis from the current project will provide recommendations to improve the students' academic curriculum pre-clinical experience. The recommendations will be provided in the form of at least three scientific publications, with one publication for each subject area intended to be evaluated (i.e., head and neck anatomy, dental anatomy, and removable prosthodontics).
Nutrient dynamics in water and soil under conventional rice cultivation in the Vietnamese Mekong Delta
Authors: Ngan Nguyen Vo Chau , Thao Huynh Van , Giang Nam Nguyen Dinh 
Published: January 2023

Background The evaluation of nutrient variability plays a crucial role in accessing soil potentials and practical intervention responses in rice production systems. Synthetic fertilizer applications and cultivation practices are considered key factors affecting nutrient dynamics and availability. Here, we assessed the nutrient dynamics in surface, subsurface water and soil under local water management and conventional rice cultivation practices in the Vietnamese Mekong Delta. Methods We implemented a field experiment (200 m 2) in the 2018 wet season and the 2019 dry season in a triple rice-cropping field. Surface water, subsurface water (30–45 cm), and topsoil (0–20 cm) were collected eight samples during the rice-growing seasons to clarify its nutrient dynamic. Results The results showed that N-NH 4 +, P-PO 4 3- and total P peaks were achieved after fertilizing. Irrespective of seasons, the nutrient content in surface water was always greater than that of subsurface water ( P<0.001), with the exception of N-NO 3 -, no significant difference was disclosed ( P>0.05). When comparing the wet and dry seasons, nutrient concentrations exhibited minor differences ( P>0.05). Under conventional rice cultivation, the effects of synthetic fertilizer topdressing on the total N, soil organic matter (SOM), and total P were negligible in the soil. Higher rates of N fertilizer application did not significantly increase soil N-NH 4 +, total N, yet larger P fertilizer amounts substantially enhanced soil total P ( P<0.001). Conclusions Under conventional rice cultivation, the low concentration of N-NH 4 +, P-PO 4 3- and total P in the subsurface water indicated that nutrient losses mainly occur through runoff rather than leaching. Notably, nutrient content in soil was fairly high, whilst SOM was varied from low to medium between seasons. Future work should consider the nutrient balance and nutrient dynamic simulation on surface and subsurface.
Determining the Accuracy of the Triangular and PERT Distributions
Authors: Khan Imran A. , Bickel J. Eric , Hammond Robert K. 
Published: January 2023

The Triangular and PERT (Program Evaluation Review Technique) distribution probability density functions are commonly used in decision and risk analyses. These distributions are popular because they are each specified by only three points (two support bounds and the mode) that are believed to be easy to assess from experts or data. In this paper, we carefully analyze how close the Triangular and PERT distributions are to other distributions sharing the same support and mode and show that the errors induced by the Triangular and PERT distributions are significant. We further show that distributions that are characterized by the median tend to provide a better fit than do those that are characterized by the mode. Funding: This research was supported by the Equinor Fellows Program and the Operating System 2.0 research program developed by the Construction Industry Institute.
Diagnostic Tools for Evaluating and Comparing Simulation-Optimization Algorithms
Authors: Eckman David J. , Henderson Shane G. , Shashaani Sara 
Published: January 2023

Simulation optimization involves optimizing some objective function that can only be estimated via stochastic simulation. Many important problems can be profitably viewed within this framework. Whereas many solvers—implementations of simulation-optimization algorithms—exist or are in development, comparisons among solvers are not standardized and are often limited in scope. Such comparisons help advance solver development, clarify the relative performance of solvers, and identify classes of problems that defy efficient solution, among many other uses. We develop performance measures and plots, and estimators thereof, to evaluate and compare solvers and diagnose their strengths and weaknesses on a testbed of simulation-optimization problems. We explain the need for two-level simulation in this context and provide supporting convergence theory. We also describe how to use bootstrapping to obtain error estimates for the estimators. History: Accepted by Bruno Tuffin, area editor for simulation. Funding: This work was supported by the National Science Foundation [Grants CMMI-2035086, CMMI-2206972, and TRIPODS+X DMS-1839346]. Supplemental Material: The software that supports the findings of this study is available within the paper and its Supplementary Information [ https://pubsonline.informs.org/doi/suppl/10.1287/ijoc.2022.1261 ] or is available from the IJOC GitHub software repository ( https://github.com/INFORMSJoC ) at [ http://dx.doi.org/10.5281/zenodo.7329235 ].
The Impact of Optimized Fleets in Transportation Networks
Authors: Battifarano Matthew , Qian Sean 
Published: January 2023

Connected technologies have engendered a paradigm shift in mobility systems by enabling digital platforms to coordinate large sets of vehicles in real time. Recent research has investigated how a small number of connected vehicles may be coordinated to reduce total system cost. However, platforms may coordinate vehicles to optimize a fleet-wide objective which is neither user nor system optimal. We study the behavior of optimized fleets in mixed traffic and find that, at small penetrations, fleets may worsen system cost relative to user equilibrium, and provide a concrete example of this paradox. Past a critical penetration level, however, optimized fleets reduce system cost in the network, up to achieving system optimal traffic flow, without need for an external subsidy. We introduce two novel notions of fleet-optimal mixed equilibria: critical fleet size for user equilibrium (CFS-UE) and critical fleet size for system optimum (CFS-SO). We demonstrate on the Sioux Falls and Pittsburgh networks that 33% and 83% of vehicles, respectively, must participate in the fleet to achieve system optimum. In Pittsburgh, we find that, although fleets permeate the network, they accumulate on highways and major arterials; the majority of origin-destination pairs are either occupied exclusively by users or by the fleet. Critical fleet size offers regulators greater insight into where fleet and system interests align, transportation planners a novel metric to evaluate road improvements, and fleet coordinators a better understanding of their efforts to optimize their fleet. History: This paper has been accepted for the Transportation Science Special Issue on Emerging Topics in Transportation Science and Logistics. Funding: This work was supported by the U.S. Department of Transportation [Mobility21] and the National Science Foundation [CMMI-1931827]. Supplemental Material: The online appendices are available at https://doi.org/10.1287/trsc.2022.1189 .
Responsivity enhancement of a PtSi photodetector with graphene by the photogating effect
Authors: Mehrfar Amir Hossein , Majd Abdollah Eslami 
Published: January 2023

In this paper, by adding graphene to the platinum silicide (PtSi) photodetector and using the photogating effect, the responsivity is significantly improved in the PtSi photodetector. In this photodetector, the PtSi layer detects the light, and the graphene increases the responsivity with the photogating effect. The responsivity of the PtSi photodetector with graphene is 1.5 A/W in the optical power of 13.6 µW. The responsivity in the PtSi photodetector with graphene and without graphene is compared. By adding graphene to the PtSi photodetector, the responsivity is much improved compared to the conventional PtSi photodetector.
τ-algorithm for gathering spectroscopic information by modeling emission line shapes: application to laser-induced plasmas
Authors: Díaz Pace D. M. , Molina M. J. 
Published: January 2023

In this work, a fitting algorithm was implemented and applied to analyze emission line shapes in laser-induced breakdown spectroscopy. By modeling emission spectral lines, the optical thickness was calculated for each line of interest and the intensity line profiles were computed and matched to measured spectra. The algorithm was applied to analyze the experimental profiles of a hydrogen

H

α

line at 6562.8 Å, and the resonant lines of Mg II at 2795.5 Å and at 2802.7 Å. Spectroscopic information was obtained about the physical processes occurring in the plasma, such as self-absorption and Stark broadening. The results demonstrated the potential of the developed method to provide valuable information in plasma spectroscopy for both fundamental and applied research.
Numerical modeling of continuous wave intracavity self-Raman lasers considering the influence of the thermal effect
Authors: Ma Yayun , Yang Fen 
Published: January 2023

A space-dependent theoretical model is developed to study the influence of the thermal effect on the characteristics of self-Raman lasers. The performances of the Raman laser are well researched by solving rate equations numerically. The simulation results show that the performance of the Raman laser can be improved by narrowing the linewidth of the fundamental field and using an output coupler with optimum transmission for 880 nm and 914 nm pump wavelengths. Also, cooling the temperature of the crystal for the 880 nm pump wavelength and heating the crystal temperature appropriately for the 914 nm pump wavelength are promising routes to further improve the Raman power.