bluuebunny/crossref_metadata_2025 huggingface dataset:
Congestion Avoidance in TCP Based on Optimized Random Forest with Improved Random Early Detection Algorithm
Authors: Kumar Ajay , Hemrajani Naveen
Published: February 2024

Transmission control protocol (TCP) ensures that data are safely and accurately transported over the network for applications that use the transport protocol to allow reliable information delivery. Nowadays, internet usage in the network is growing and has been developing many protocols in the network layer. Congestion leads to packet loss, the high time required for data transmission in the TCP protocol transport layer for end-to-end connections is one of the biggest issues with the internet. An optimized random forest algorithm (RFA) with improved random early detection (IRED) for congestion prediction and avoidance in transport layer is proposed to overcome the drawbacks. Data are initially gathered and sent through data pre-processing to improve the data quality. For data pre-processing, KNN-based missing value imputation is applied to replace the values that are missing in raw data and [Formula: see text]-score normalization is utilized to scale the data in a certain range. Following that, congestion is predicted using an optimized RFA and whale optimization algorithm (WOA) is used to set the learning rate as efficiently as possible in order to reduce error and improve forecast accuracy. To avoid congestion, IRED method is utilized for a congestion-free network in the transport layer. Performance metrics are evaluated and compared with the existing techniques with respect to accuracy, precision, recall, specificity, and error, whose values that occur for the proposed model are 98%, 98%, 99%, 98%, and 1%. Throughput and latency are also evaluated in the proposed method to determine the performance of the network. Finally, the proposed method performs better when compared to the existing techniques and prediction, and avoidance of congestion is identified accurately in the network.
Faster MIL-based Subgoal Identification for Reinforcement Learning by Tuning Fewer Hyperparameters
Authors: Sunel Saim , Çilden Erkin , Polat Faruk
Published: February 2024

Various methods have been proposed in the literature for identifying subgoals in discrete reinforcement learning (RL) tasks. Once subgoals are discovered, task decomposition methods can be employed to improve the learning performance of agents. In this study, we classify prominent subgoal identification methods for discrete RL tasks in the literature into the following three categories: graph-based, statistics-based, and multi-instance learning (MIL)-based. As contributions, first, we introduce a new MIL-based subgoal identification algorithm called EMDD-RL and experimentally compare it with a previous MIL-based method. The previous approach adapts MIL’s Diverse Density (DD) algorithm, whereas our method considers Expected-Maximization Diverse Density (EMDD). The advantage of EMDD over DD is that it can yield more accurate results with less computation demand thanks to the expectation-maximization algorithm. EMDD-RL modifies some of the algorithmic steps of EMDD to identify subgoals in discrete RL problems. Second, we evaluate the methods in several RL tasks for the hyperparameter tuning overhead they incur. Third, we propose a new RL problem called key-room and compare the methods for their subgoal identification performances in this new task. Experiment results show that MIL-based subgoal identification methods could be preferred to the algorithms of the other two categories in practice.
On the Value of Head Labels in Multi-Label Text Classification
Authors: Wang Haobo , Peng Cheng , Dong Hede , Feng Lei , Liu Weiwei , Hu Tianlei , Chen Ke , Chen Gang
Published: February 2024

A formidable challenge in the multi-label text classification (MLTC) context is that the labels often exhibit a long-tailed distribution, which typically prevents deep MLTC models from obtaining satisfactory performance. To alleviate this problem, most existing solutions attempt to improve tail performance by means of sampling or introducing extra knowledge. Data-rich labels, though more trustworthy, have not received the attention they deserve. In this work, we propose a multiple-stage training framework to exploit both model- and feature-level knowledge from the head labels, to improve both the representation and generalization ability of MLTC models. Moreover, we theoretically prove the superiority of our framework design over other alternatives. Comprehensive experiments on widely used MLTC datasets clearly demonstrate that the proposed framework achieves highly superior results to state-of-the-art methods, highlighting the value of head labels in MLTC.
3D Traction Force Microscopy in Biological Gels: From Single Cells to Multicellular Spheroids
Authors: Cheung Brian C.H. , Abbed Rana J. , Wu Mingming , Leggett Susan E.
Published: February 2024

Cell traction force plays a critical role in directing cellular functions, such as proliferation, migration, and differentiation. Current understanding of cell traction force is largely derived from 2D measurements where cells are plated on 2D substrates. However, 2D measurements do not recapitulate a vital aspect of living systems; that is, cells actively remodel their surrounding extracellular matrix (ECM), and the remodeled ECM, in return, can have a profound impact on cell phenotype and traction force generation. This reciprocal adaptivity of living systems is encoded in the material properties of biological gels. In this review, we summarize recent progress in measuring cell traction force for cells embedded within 3D biological gels, with an emphasis on cell–ECM cross talk. We also provide perspectives on tools and techniques that could be adapted to measure cell traction force in complex biochemical and biophysical environments.
Intervention Optimization: A Paradigm Shift and Its Potential Implications for Clinical Psychology
Authors: Collins Linda M. , Nahum-Shani Inbal , Guastaferro Kate , Strayhorn Jillian C. , Vanness David J. , Murphy Susan A.
Published: February 2024

To build a coherent knowledge base about what psychological intervention strategies work, develop interventions that have positive societal impact, and maintain and increase this impact over time, it is necessary to replace the classical treatment package research paradigm. The multiphase optimization strategy (MOST) is an alternative paradigm that integrates ideas from behavioral science, engineering, implementation science, economics, and decision science. MOST enables optimization of interventions to strategically balance effectiveness, affordability, scalability, and efficiency. In this review we provide an overview of MOST, discuss several experimental designs that can be used in intervention optimization, consider how the investigator can use experimental results to select components for inclusion in the optimized intervention, discuss the application of MOST in implementation science, and list future issues in this rapidly evolving field. We highlight the feasibility of adopting this new research paradigm as well as its potential to hasten the progress of psychological intervention science.
Oral Astringency in Plant Proteins: An Underestimated Issue in Formulating Next-Generation Plant-Based Foods
Authors: Sarkar Anwesha
Published: February 2024

Ensuring the supply of affordable, palatable, healthy, and sustainable nutrients to feed the growing population without transgressing the planetary boundaries remains a key challenge in the food science community. A dietary transition toward low-emission, plant-based foods, with less reliance on animal agriculture, is advocated for sustainability, health, and ethical reasons. A major hurdle for mainstream adoption of plant-based foods is their poor sensorial performance, such as nonjuicy and astringent textures as well as various off-flavors. This review presents the current understanding of astringency and oral friction of plant-based foods. It focuses on plant proteins and their application in plant-based meat and dairy analogs. In addition, the latest advances in the quantitative characterization of astringency using tribology, electrochemistry, and cellular tools are covered. Finally, we examine factors influencing astringency and propose easy-to-implement colloidal strategies that may mitigate astringency issues, thereby underpinning the design of the next generation of sustainable and pleasurable plant-based foods.
Efficient Amperometric Detection of H2O2 using Gold Nanoparticle decorated Polythiophene/Hematite Ore Nanocomposite
Authors: Rashed Md. A. , Rahman M. Hafizur , Nayem N. I. , Ahmed Jahir , Faisal M. , Jalalah Mohammed , Harraz Farid A.
Published: February 2024

In the present work, we developed a cheap and sensitive H2O2 electrochemical sensor. Herein we fabricated an electrochemical sensor electrode using a naturally extracted hematite ore decorated with conducting polythiophene (Pth) and gold nanoparticles (AuNPs). A simple synthesis route was adopted for the electrocatalyst synthesis, where Pth was synthesized through oxidative polymerization and then combined with Hematite Ore nanostructure via a simple ultrasonication process. Later a simple photo-reduction approach was used to develop a 1%Au@5%Pth/Hematite Ore nanocomposite. The as-fabricated Au@Pth/Hematite Ore nanocomposite was successfully characterized by applying X-ray diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS), High-Resolution Transmission Electron Microscope (HR-TEM), and Field Emission Scanning Electron Microscope (FE-SEM) techniques. The obtained results reveal that undoped naturally extracted hematite ore is composed of Fe2O3 and Fe3O4 phases. The catalytic efficiency of the newly designed nanocomposite and its sensing ability towards H2O2 were assessed using electrochemical techniques including electrochemical impedance spectroscopy (EIS), cyclic voltammetry (CV), linear sweep voltammetry (LSV) and highly sensitive amperometric (i-t) techniques. The Au@Pth/Hematite Ore/GCE sensor showed a wide linear dynamic range of 0.50–9.50 mM with high sensitivity of 69.18 μAmM−1cm−2. The limit of detection (LOD) was estimated to be 5.18 μM. The examined sensor demonstrated acceptable reproducibility, repeatability as well as stability. The sensor electrode also showed anti-interference behavior in the presence of different inorganic and organic interfering ions or molecules during the H2O2 determination. Moreover, the proposed sensor exhibits acceptable recovery of H2O2 in real sample analysis. Hence, this novel sensor is regarded as a promising contender in scientific and industrial domains.
Communication—Controlling Etching of Germanium through Surface Charge Manipulation
Authors: Wood Joseph G. , Mitsyuk Surge , Brayfield Cassondra , Carpenter Arthur , Hunt Charles E. , van Benthem Klaus
Published: February 2024

Potassium hydroxide (KOH) aqueous solutions can effectively etch germanium. Etch rates were determined in an electrolytic etch cell. Electrically isolated Ge wafers were subject to an etch rate of 1.45 ± 0.07 nm min−1, increasing to 12.6 ± 0.2 nm min−1 when grounded, 97 ± 2 nm min−1 when biased at −0.9 V, and 138 ± 2 nm min−1 with periodic biasing. Results suggest that the previously reported limited etching in KOH is associated with the recombination of holes with electrons injected from the surface reaction. The results of this study demonstrate that changing the hole concentration through biasing is an effective tool to control electrolytic etch rates, enabling future selective etching processes for germanium.
Assemblages and Subassemblages of Giardia duodenalis in Rural Western, Kenya: Association with Sources, Signs, and Symptoms
Authors: Barasa Erick , Indieka Briston , Shaviya Nathan , Osoro Ezra , Maloba Geofrey , Mukhongo Denis , Budambula Valentine , Were Tom
Published: February 2024

Background. Giardia duodenalis causes sporadic or epidemic infections in humans. The parasite comprises assemblages A-H with A and B subdivided further into AI-IV and BI-IV subassemblages. Attempts aimed at linking these genotypes with sources and gastrointestinal manifestations of the infection are largely unexplored in rural communities. Methods. In this cross-sectional study, G. duodenalis infection was genotyped and associated with sources, and gastrointestinal signs and symptoms of the disease among residents of Busia County, a rural setting in western Kenya. Demographic and clinical information were captured using standardized forms. Stool specimens were obtained from the patients and used for genotyping at glutamate dehydrogenase and triose-phosphate isomerase loci using the polymerase chain reaction and restriction fragment length polymorphism. Results. Assemblage B (63.6%) was the most prevalent G. duodenalis infection, while A (20.5%) and mixed A/B (15.9%) were also detected. Among the subassemblages, AI (5.7%), AII (8.0%), AIII (3.4), BIII (30.7%), and BIV (17.0%) were diagnosed including the mixed AII/BIII (15.9%), BIII/BIV (15.9%), AI/AIII (2.3%), and AI/AII (1.1%) infections. Binary logistic regression indicated associations for assemblage A with stomach upset, history of nitroimidazole treatment, and residing in a homestead with cattle and B with age<18 years, history of eating outdoors, vomiting, steatorrhea, and residing in a homestead with cattle, goats, and poultry (p<0.05 for all). Among the subassemblages, associations were found for AI with residing in a homestead having cattle and history of nitroimidazole treatment, BIII with residing in a homestead having cattle and poultry, and BIV with steatorrhea (p<0.05 for all). Altogether, this study illustrates that G. duodenalis assemblage B and subassemblage BIII are the most predominant and are linked to age<18 years, gastrointestinal manifestations, and living in a homestead with domestic ruminants and poultry. Conclusion. Targeted mass prophylactic treatment of domestic animals and utilization of gastrointestinal presentations, age<18 years, and a history of nitroimidazole use are useful in the diagnosis and prevention of giardiasis among residents of rural communities.
A Short Post-Reattachment Ultrasensitive Window of Time in Human Cancer Cells as Therapeutic Target of Prolonged Low-Dose Administration of Specific Compounds
Authors: Guishard Ashley Rebecca , Guishard Alecia Florence , Semenova Nina , Kaushik Vivek , Azad Neelam , Iyer Anand K. V. , Yakisich Juan Sebastian
Published: February 2024

Prolonged low-dose administration (PLDA) of several FDA-approved drugs for noncancer conditions or dietary compounds is associated with a lower incidence of specific types of cancers and with the lower formation of metastasis. However, the underlying mechanism is unknown; there is a discrepancy between the concentration of drugs needed to kill cancer cells in vitro and the actual serum levels (10 and >1000 times lower) found in patients. In this study, we evaluated the hypothesis that clonogenicity may be the target of PLDA. We compared the effect of nigericin (NIG) and menadione (MEN) on the human A549 and H460 lung and MCF-7 and MDA-MB-231 breast cancer cell lines using routine MTT and colony forming assays (CFA). The ability of both NIG and MEN to eliminate 100% of cancer cells was at least 2-10 times more potent in CFA compared to MTT assays. Our results revealed the existence of a short post-reattachment window of time when cancer cells growing at low density are more sensitive to PLDA of specific drugs likely by targeting clonogenic rather than proliferation pathways. This short ultrasensitive window of time (SUSWoT) was cell- and drug-type specific: the SUSWoT for NIG was present in H460, A549, and MDA-MB-231 cells but not evident in MCF-7 cells. Conversely, a similar SUSWoT for MEN was present in MCF-7, MDA-MD-231, and A549 cells but not evident in H460 cells. Our findings partially explain the decreased incidence of specific types of cancer by PLDA of FDA-approved drugs (or dietary compounds) for noncancer conditions.
Solving Large-Scale Unconstrained Optimization Problems with an Efficient Conjugate Gradient Class
Authors: Bojari Sanaz , Paripour Mahmoud
Published: February 2024

The main goal of this paper is to introduce an appropriate conjugate gradient class to solve unconstrained optimization problems. The presented class enjoys the benefits of having three free parameters, its directions are descent, and it can fulfill the Dai–Liao conjugacy condition. Global convergence property of the new class is proved under the weak-Wolfe–Powell line search technique. Numerical efficiency of the proposed class is confirmed in three sets of experiments including 210 test problems and 11 disparate conjugate gradient methods.
Prioritizing Asthma Treatment Drugs through Multicriteria Decision Making
Authors: Sultana Sobia
Published: February 2024

Asthma is a medical condition characterized by inflammation, narrowing, and swelling of a person’s airways, leading to increased mucus production and difficulties in breathing. Topological indices are instrumental in assessing the physical and chemical attributes of these asthma drugs. As resistance to current treatments continues to emerge and undesirable side effects are linked to certain medications, the search for novel and enhanced drugs becomes a top priority. In this study, the examination of 19 distinct asthma medications was focused. In this study, quantitative structure-activity relationship (QSAR) and quantitative structure-property relationship (QSPR) modeling, in combination with multicriteria decision-making (MCDM) technique VIKOR (VIekriterijumsko KOmpromisno Rangiranje) were employed on asthma drugs, to achieve the most favorable rankings for each asthma drug, taking into account their distinct properties. The topological indices employed for QSPR modeling were Randic index, reciprocal Randic index, Zagreb indices, hyper-Zagreb index, harmonic index, geometric arithmetic index, and forgotten index.
Autonomous Identification of Bridge Concrete Cracks Using Unmanned Aircraft Images and Improved Lightweight Deep Convolutional Networks
Authors: Song Fei , Sun Ying , Yuan Guixia
Published: February 2024

The identification of the development of structural defects is an important part of bridge structure damage diagnosis, and cracks are considered the most typical and highly dangerous structural disease. However, existing deep learning‐based methods are mostly aimed at the scene of concrete cracks, while they rarely focus on designing network architectures to improve the vision‐based model performance from the perspective of unmanned aircraft system (UAS) inspection, which leads to a lack of specificity. Because of this, this study proposes a novel lightweight deep convolutional neural network‐based crack pixel‐level segmentation network for UAS‐based inspection scenes. Firstly, the classical encoder‐decoder architecture UNET is utilized as the base model for bridge structural crack identification, and the hourglass‐shaped depthwise separable convolution is introduced to replace the traditional convolutional operation in the UNET model to reduce model parameters. Then, a kind of lightweight and efficient channel attention module is used to improve model feature fuzzy ability and segmentation accuracy. We conducted a series of experiments on bridge structural crack detection tasks by utilizing a long‐span bridge as the research item. The experimental results show that the constructed method achieves an effective balance between reasoning accuracy and efficiency with the value of 97.62% precision, 97.23% recall, 97.42% accuracy, and 93.25% IOU on the bridge concrete crack datasets, which are significantly higher than those of other state‐of‐the‐art baseline methods. It can be inferred that the application of hourglass‐shaped depth‐separable volumes can actively reduce basic model parameters. Moreover, the lightweight and efficient attention modules can achieve local cross‐channel interaction without dimensionality reduction and improve the network segmentation performance.
Inhibition of YAP1 Rescues Erectile Dysfunction by Inhibiting Phenotypic Modulation through Myocardin in Diabetic Rats
Authors: Lin Yangyan , Hui Jialiang , Pan Miaoxia , Wang Li , Luo Junqi , Chen Zerong , Zhang Haibo , Wei Anyang
Published: February 2024

Background. Phenotypic modulation was shown to be related to the pathological mechanism of diabetes mellitus erectile dysfunction (DMED), and excessive expression of YAP1 was measured in the cavernous tissues of rats with DMED. Objectives. This investigation was performed to explore the efficiency and mechanism of gene therapy through the knockdown of YAP1 in the field of ED treatment. Materials and Methods. Corpus cavernosum smooth muscle cells were obtained and cultivated in vitro employing the explant technique. EdU, CCK‐8, and collagen gel lattice contraction assays were subsequently performed to assess cell proliferation and contractility, which indicate smooth muscle phenotypes. Results. Initially, overexpression of YAP1 enhanced the proliferation and expression of YAP1 and osteopontin (OPN) while reducing cell contractility and the expression of myocardin, α‐SMA, and calpontin, which is consistent with phenotypic modulation. Moreover, knocking down YAP1 resulted in the opposite effects, and the blockade of myocardin attenuated the reversal of phenotypic transformation. Then, 45 screened DMED rats were randomly divided into three equal groups, named streptozotocin (STZ)‐induced DMED with intracavernosal injection of Ad‐myocardin (DMED + myocardin), DMED with lenti‐shYAP1 (DMED + shYAP1) and DMED with PBS (DMED + PBS), and 10 rats were in the negative control group. Staining with H&E and Masson’s trichrome, immunochemistry, and determination of the ratio of the intracavernosal pressure/mean arterial pressure were performed to evaluate penile erection and histological changes. Western blotting was conducted to determine the molecular protein expression levels. In vivo, similar to myocardin overexpression, YAP1 inhibition rescued erectile function, repaired morphology, and maintained the contractile phenotype of smooth muscle tissues 14 days after treatment. Discussion and Conclusion. In conclusion, our study demonstrated the validity of gene therapy by downregulating excessive YAP1 expression to ameliorate ED in diabetic rats, and the ability of YAP1 inhibition to reverse phenotypic modulation was mediated through interaction with myocardin.
TABLE 4 from Real-world Trends, Rural-urban Differences, and Socioeconomic Disparities in Utilization of Narrow versus Broad Next-generation Sequencing Panels
Authors: Zhao Yiqing , Dimou Anastasios , Fogarty Zachary C. , Jiang Jun , Liu Hongfang , Wong William B. , Wang Chen
Published: February 2024

Association of area deprivation index and urban/rural status with clinical trial matching (success vs. failed)a
Supplementary Table 7 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset
Authors: Wang Cankun , Ma Anjun , Li Yingjie , McNutt Megan E. , Zhang Shiqi , Zhu Jiangjiang , Hoyd Rebecca , Wheeler Caroline E. , Robinson Lary A. , Chan Carlos H.F. , Zakharia Yousef , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Denko Nicholas , Tinoco Gabriel , Husain Marium , Jin Ning , Osman Afaf E.G. , Eljilany Islam , Tan Aik Choon , Coleman Samuel S. , Denko Louis , Riedlinger Gregory , Schneider Bryan P. , Spakowicz Daniel , Ma Qin
Published: February 2024

Phylogenetic relationships of microbial signatures.
TABLE 2 from Real-world Trends, Rural-urban Differences, and Socioeconomic Disparities in Utilization of Narrow versus Broad Next-generation Sequencing Panels
Authors: Zhao Yiqing , Dimou Anastasios , Fogarty Zachary C. , Jiang Jun , Liu Hongfang , Wong William B. , Wang Chen
Published: February 2024

Time to test return (turnaround time) for large panel, medium panel, and single-gene genomic tests
Supplementary Table 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset
Authors: Wang Cankun , Ma Anjun , Li Yingjie , McNutt Megan E. , Zhang Shiqi , Zhu Jiangjiang , Hoyd Rebecca , Wheeler Caroline E. , Robinson Lary A. , Chan Carlos H.F. , Zakharia Yousef , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Denko Nicholas , Tinoco Gabriel , Husain Marium , Jin Ning , Osman Afaf E.G. , Eljilany Islam , Tan Aik Choon , Coleman Samuel S. , Denko Louis , Riedlinger Gregory , Schneider Bryan P. , Spakowicz Daniel , Ma Qin
Published: February 2024

Identified cancer-associated microbial signatures in all studied cancer types.
Supplementary Figure 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset
Authors: Wang Cankun , Ma Anjun , Li Yingjie , McNutt Megan E. , Zhang Shiqi , Zhu Jiangjiang , Hoyd Rebecca , Wheeler Caroline E. , Robinson Lary A. , Chan Carlos H.F. , Zakharia Yousef , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Denko Nicholas , Tinoco Gabriel , Husain Marium , Jin Ning , Osman Afaf E.G. , Eljilany Islam , Tan Aik Choon , Coleman Samuel S. , Denko Louis , Riedlinger Gregory , Schneider Bryan P. , Spakowicz Daniel , Ma Qin
Published: February 2024

Upset plot of overall identified species in 12 cancer types.
FIGURE 3 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset
Authors: Wang Cankun , Ma Anjun , Li Yingjie , McNutt Megan E. , Zhang Shiqi , Zhu Jiangjiang , Hoyd Rebecca , Wheeler Caroline E. , Robinson Lary A. , Chan Carlos H.F. , Zakharia Yousef , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Denko Nicholas , Tinoco Gabriel , Husain Marium , Jin Ning , Osman Afaf E.G. , Eljilany Islam , Tan Aik Choon , Coleman Samuel S. , Denko Louis , Riedlinger Gregory , Schneider Bryan P. , Spakowicz Daniel , Ma Qin
Published: February 2024

Network visualization of identified microbial communities in COAD and THCA. The cancer-type nodes were highlighted by an octagon shape, while the microbial species nodes were highlighted in a circle shape. The thickness of the edges in the network reflects the attention weight scores, indicating the strength of the relationship between the species and cancer. In addition, the metabolic compound nodes were highlighted with a yellow triangle shape, while the phylogenetic relationship edges were highlighted in gray. A, COAD-associated microbes highlighted with metabolic compound. B, THCA-associated microbes highlighted with metabolic compound. C, COAD-associated microbes highlighted with phylogenetic relationships. D, THCA-associated microbes highlighted with phylogenetic relationships.
FIGURE 1 from A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset
Authors: Wang Cankun , Ma Anjun , Li Yingjie , McNutt Megan E. , Zhang Shiqi , Zhu Jiangjiang , Hoyd Rebecca , Wheeler Caroline E. , Robinson Lary A. , Chan Carlos H.F. , Zakharia Yousef , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Denko Nicholas , Tinoco Gabriel , Husain Marium , Jin Ning , Osman Afaf E.G. , Eljilany Islam , Tan Aik Choon , Coleman Samuel S. , Denko Louis , Riedlinger Gregory , Schneider Bryan P. , Spakowicz Daniel , Ma Qin
Published: February 2024

Overview of the MEGA workflow. Four main steps were included in carrying out model training and biological gene network inference. MEGA uses ORIEN datasets and two database dependencies as the data sources. Preprocessing steps are employed to generate AI-ready data for graph neural network training. After deep learning model training, the cancer-associated microbial signatures were selected on the basis of the attention scores of each species at the sample level. The final results of the identified cancer-associated microbial communities have been provided in a tabular format and are available for additional visualization.
Data from Real-world Trends, Rural-urban Differences, and Socioeconomic Disparities in Utilization of Narrow versus Broad Next-generation Sequencing Panels
Authors: Zhao Yiqing , Dimou Anastasios , Fogarty Zachary C. , Jiang Jun , Liu Hongfang , Wong William B. , Wang Chen
Published: February 2024

Abstract
Advances in genetic technology have led to the increasing use of genomic panels in precision oncology practice, with panels ranging from a couple to hundreds of genes. However, the clinical utilization and utility of oncology genomic panels, especially among vulnerable populations, is unclear. We examined the association of panel size with socioeconomic status and clinical trial matching. We retrospectively identified 9,886 eligible adult subjects in the Mayo Clinic Health System who underwent genomic testing between January 1, 2016 and June 30, 2020. Patient data were retrieved from structured and unstructured data sources of institutional collections, including cancer registries, clinical data warehouses, and clinical notes. Socioeconomic surrogates were approximated using the Area Deprivation Index (ADI) corresponding to primary residence addresses. Logistic regression was performed to analyze relationships between ADI or rural/urban status and (i) use of genomic test by panel size; (ii) clinical trial matching status. Compared with patients from the most affluent areas, patients had a lower odds of receiving a panel test (vs. a single-gene test) if from areas of higher socioeconomic deprivation [OR (95% confidence interval (CI): 0.71 (0.61–0.83), P < 0.01] or a rural area [OR (95% CI): 0.85 (0.76–0.96), P < 0.01]. Patients in areas of higher socioeconomic deprivation were less likely to be matched to clinical trials if receiving medium panel tests [(OR) (95% CI): 0.69 (0.49–0.97), P = 0.03]; however, there was no difference among patients receiving large panel tests (P > 0.05) and rural patients were almost 2x greater odds of being matched if receiving a large panel test [(OR) (95% CI): 1.76 (1.21–2.55), P < 0.01].
Significance:
We identified socioeconomic and rurality disparities in the use of genomic tests and trial matching by panel size, which may have implications for equal access to targeted therapies. The lack of association between large panel tests and clinical trial matching by socioeconomic status, suggests a potential health equity impact, while removing barriers in access to large panels for rural patients may improve access to trials. However, further research is needed.
Predictors and Prognostic Impact of Early Acute Kidney Injury in Cardiogenic Shock: Results from a Monocentric, Prospective Registry
Authors: Schupp Tobias , Behnes Michael , Rusnak Jonas , Weidner Kathrin , Ruka Marinela , Dudda Jonas , Schmitt Alexander , Forner Jan , Egner-Walter Sascha , Ayasse Niklas , Bertsch Thomas , Kittel Maximilian , Akin Ibrahim
Published: February 2024

Introduction: The presence of acute kidney injury (AKI) was shown to increase the risk of mortality following acute myocardial infarction (AMI), however, data regarding the prognostic impact of AKI in patients with concomitant cardiogenic shock (CS) is limited. The study investigates predictors and the prognostic impact of AKI in patients with CS.
Methods: Consecutive patients with CS from 2019 to 2021 were included at one institution. Laboratory values were retrieved from day of disease onset (day 1) and days 2, 3, 4 and 8 thereafter. Predictors for AKI (defined as an increase of plasma creatinine > 50% within 48 h reffering to pre-admission or baseline creatinine on day 1 and/or the need for continuous veno-venous haemodiafiltration (CVVHDF)) and the prognostic impact of AKI with regard to 30-day all-cause mortality were assessed. Statistical analyses included univariable t-test, Spearman´s correlation, C-statistics, Kaplan-Meier and Cox proportional regression analyses.
Results: 219 CS patients were included with an incidence of CS-related AKI of 52%. With an area under the curve (AUC) up to 0.689 (p =0.001), creatine discriminated 30-day mortality in CS. Increasing lactate levels (OR = 1.194; 95% CI 1.083 – 1.316; p = 0.001; per increase of 1 mmol/l) was associated with the occurence of AKI. The presence of AKI was associated with an increased risk of 30-day all-cause mortality (63% vs. 36%; HR = 2.138; 95% CI 1.441 – 3.171 p = 0.001), even after multivariable adjustment (HR = 1.861; 95% CI 1.207 – 2.869; p = 0.005). Finally, highest risk of all-cause mortality was observed in patients with AKI requiring CVVHDF (75% vs. 44%; log rank p = 0.001; HR = 2.211; 95% CI 1.315 – 3.718; p = 0.003).
Conclusion: AKI affects more than half of patients with CS and is independently associated with 30-day all-cause mortality in CS, with highest risk of death among patients with AKI requiring CVVHDF.
How Might the Number of Lymph Nodes Removed during RARP Impact the Postoperative Outcomes?
Authors: Farzat Mahmoud , Wagenlehner Florian M.
Published: February 2024

Introduction: Symptomatic lymphocele remains a relevant complication after pelvic tumor surgery. This study aims to investigate how the number of lymph nodes removed may influence postoperative outcomes and if it increases the probability of detecting lymph node metastasis. Methods: The study included 500 patients who underwent RARP including lymphadenectomy performed by a single surgeon. Patients were divided into two groups: group 1 consisted of 308 patients with 20 or fewer lymph nodes removed (mean 15), while group 2 had 192 patients with over 20 nodes removed (mean 27). Perioperative data were analyzed, and postoperative outcomes were compared between groups. Results: Overall, lymph node metastasis was detected in 17.8% of men. In detail, out of 19.6 lymph nodes removed, an average of 3.14 lymph nodes per patient showed metastasis, with a slightly higher incidence of 19.7% in group 2 compared to 16.5% in group 1, though not statistically significant (p = 0.175). The number of lymph node metastases was significantly higher in group 2 patients (3.47) versus group 1 (2.37) (p = 0.048). All complications except symptomatic lymphoceles (p = 0.004) were not significantly different between groups. Univariate linear regression analysis revealed no correlation between the number of removed lymph nodes and symptomatic lymphocele. However, it did correlate with catheter days and readmissions. Conclusion: A correlation may exist between the number of lymph nodes removed during RARP and an increased incidence of complications, particularly symptomatic lymphocele. A more extensive PLND may result in prolonged catheter days and increased readmissions. With the increased extent of pelvic lymphadenectomy, the probability of detecting lymphogenic metastasis rises. The diagnostic value of PLND is well established. Further randomized trials are needed to weigh its necessity and extent.
Insect galls of the Chapada Diamantina, Rio de Contas, Bahia, Brazil
Authors: Araújo Tainar de Jesus , Maia Valéria Cid , Carneiro Marco Antonio Alves , Santos-Silva Juliana
Published: February 2024

We surveyed insect galls and their host plants in areas of Caatinga and Cerrado in the municipality of Rio de Contas, in the extreme south of the Chapada Diamantina (Bahia state), between 703 and 1,897 m altitude, in order to contribute to the knowledge and conservation of local biodiversity. The survey was conducted in eight locations, adopting the random walking methodology for sampling, four in Caatinga and four in Cerrado, covering distinct phytophysiognomies (cerrado sensu stricto, gallery forest, shrubby caatinga, riparian forest, and rocky field). Eighty-four different insect gall morphotypes were reported, 48 (57.14%) of them on 42 host species in Cerrado and 36 (42.86%) on 24 host species in Caatinga. Most galls occurred on leaves (48.72%) and were globoid (53.76%), glabrous (52.92%), isolated (55.44%), usually one-chambered (61.32%), and brown (25.2%). The gall-inducing insects identified belonged to Lepidoptera (n = 1), Thysanoptera (n = 1), Hemiptera (n = 2), and Diptera (Cecidomyiidae) (n = 16). This was the first inventory of galls in the Chapada Diamantina, so all records are new for the region. We also recorded the first occurrences of galls on two Cerrado plant species and on two in the Caatinga. We found a significant positive correlation between gall richness and plant species richness, suggesting that radiation of gall-inducing insects may be associated with plant species richness.
Five new species of Asphondylia (Diptera, Cecidomyiidae, Asphondyliini) from Brazilian restinga (Atlantic Forest)
Authors: Maia Valéria Cid
Published: February 2024

Asphondylia braziliensis sp. nov., Asphondylia fluminensis sp. nov., Asphondylia marambaiensis sp. nov., Asphondylia varroniae sp. nov., and Asphondylia xerezi sp. nov., are described based on material from Brazilian restingas. The first species induces galls on Struthanthus acuminatus (Ruiz. & Pav.) Kuijt (Loranthaceae), the second on Erythroxylum ovalifolium Peyr (Erythroxylaceae), the third on Lantana fucata Lindl. (Verbenaceae), the fourth on Varronia curassavica Jacq. (Cordiaceae), and the fifth on Heliotropium sp. (Heliotropiaceae). One host plant, Erythroxylum ovalifolium, is endemic to the Atlantic forest. The other plant species are native to Brazil. Illustrations of relevant morphological characters are provided. The new species are compared with congeneric Neotropical species. Types are deposited in the Entomological Collection of the Museu Nacional, Rio de Janeiro.
Diversity of insect galls in veredas of the Brazilian Cerrado in Minas Gerais, Brazil
Authors: Grandez-Rios Julio Miguel , Rhie Matthias Yunsu , Costa Leonardo Vinicius Ataíde , Gonçalves Maria Fernanda , Araújo Walter Santos de
Published: February 2024

Brazilian veredas are hygrophilous communities with high species diversity, featuring many floristic studies but a still incipient number of faunistic studies. In the present study, we conducted an inventory of insect galls in four different veredas located in the Northern region of Minas Gerais, Brazil. Overall, we found 75 gall morphotypes, distributed across 50 host species representing 37 plant genera and 22 families. Fabaceae was the plant family with the greatest number of insect gall morphotypes (n = 21), followed by Malpighiaceae (n = 10). The plant genera that supported the highest diversity of insect galls were Copaifera (n = 8) and Byrsomima (n = 5). The plant species Copaifera oblongifolia (n = 6) and Anacardium humile (n = 4) exhibited the highest richness of insect galls. The leaves were the most attacked organs (89% of all galls). Most morphotypes are glabrous (83%), green (69%) and lenticular (60%). The taxa of gall-inducing insects were identified for 46 morphotypes (80%), and were recorded inducers from the orders Diptera, Lepidoptera, and Hymenoptera. Cecidomyiidae (Diptera) was the most representative galling group, with 42 morphotypes, making up 93.3% of the recorded inducers. Among the sampled veredas areas, the Vereda do Peruaçu presented the highest richness of insect gall morphotypes and host plant species. The faunistic similarity was higher in the Pedras and Tiririca veredas, followed by Almescla and Peruaçu veredas. This is the first systematic inventory of insect galls and their host plant in Brazilian veredas. The diversity of insect galls in the studied veredas is relatively high when compared to other Brazilian Cerrado vegetation types.
O romance como arena de disputas sociais: notas sobre Cacau e Terras do sem-fim
Authors: Santos Neto Evandro Jose dos Santos
Published: February 2024

The text proposes a reading, from a comparative perspective, of the novels Cacau and Terras do sem-fim, by Jorge Amado, using as a research method some definitions associated with the proletarian novel and the modern novel. The aim is to verify how the complex social structures are analyzed, considering the figuration of the worker linked to the legacy of slaveholding patriarchy that defines sociocultural relations and working conditions in Brazil at the beginning of the 20th century.
O potencial da obra literária de Jorge Amado: cenários, tempos, personagens e enredos
Authors: Andrade Celeste Maria Pacheco de , Andrade Ana Claudia Pacheco de
Published: February 2024

O presente artigo analisa o potencial da obra literária de Jorge Amado reconhecendo-a como acervo e fonte para a pesquisa histórica, ao enfatizar dois temas: luta entre explorados e exploradores e relações etnicorraciais. Na interface entre a Literatura e a História, reconhece a atualidade e o alcance da obra para além da sua narrativa.
Abc de Castro Alves, de Jorge Amado: canto de liberdade, sertão e projeto literário
Authors: Piaulino Ingrid , Lobato Andrea , Lima Welistony Câmara , Martins Ana Patrícia Sá
Published: February 2024

Jorge Amado's Abc de Castro Alves narrates the life of the Bahian poet and builds him as a character, aiming at the exaltation of an engaged Brazilian literature. Thus, we seek to understand how Alves is woven as a literary element, his relationship with Jorge Amado's literary/political project and the idea of sertão as a libertarian field. To this end, the methodology used was qualitative and bibliographic, listing Rossi (2009), Pontes (2017) and Figueiredo (1998). This research is justified by the sharing of the dialog between Jorge Amado and the poetic work of Castro Alves who, although they are subjects of different times, are guided by the ideational construct of freedom.
FRACTO 111: uma experiência sobre estéticas insurgentes e o abolicionismo penal
Authors: Gaulês Murilo Moraes
Published: February 2024

Este artigo aborda as experiências do processo criativo da ação performativa FRACTO 111 e seus desdobramentos políticos, estéticos e visionários. A partir da perspectiva da metodologia de ficções visionárias, elaborada pela artista e abolicionista penal americana Walidah Imarisha, o trabalho reforça as relações entre arte e vida e apresenta possibilidades do engajamento das visualidades da cena na luta antiprisional e abolicionista penal.
Ampliar o visível: a lógica do som e da cor
Authors: Pitozzi Enrico , Gusmão Cynthia
Published: February 2024

O texto de Enrico Pitozzi, professor do Departamento de Artes da Universidade de Bolonha, aborda as relações entre imagem acústica e imagem visível na obra do encenador Romeo Castellucci e da Socìetas Raffaello Sanzio, em parceria com o compositor Scott Gibbons. Pitozzi relaciona a questão com aspectos da teoria das atmosferas de Gernot Böhme.
ECDYSIS: embalagens, maquiagens, mortalhas, entre outras linguagens do corpo-máscara
Authors: Schwarz Erika
Published: February 2024

Este artigo, resultado da pesquisa de doutorado homônima, apresenta mascaramentos que reconfiguram e expandem o corpo em contextos performativos, buscando contribuir com pensamentos sobre os atos de vestir nas artes vivas contemporâneas. Segundas peles elásticas, máscaras de gesso, capas e invólucros plásticos são tratados como vestíveis e problematizados nos trabalhos de Hélio Oiticica, Lygia Pape, Eleonora Fabião, Tadeusz Kantor e Regina José Galindo, em diálogo com Lea Vergine, Gilles Deleuze e Félix Guattari, Michel Foucault, entre outros, transbordando a noção tradicional de figurino e aproximando a composição corpo-máscara de outras imagens que afirmam a relação arte-vida, tais como casulo, bolsa amniótica, embalagem e mortalha.
Espaço-tempo fluido: entrelaçamentos entre a cenografia digital, performance e animismo
Authors: Cunha Christiane Lopes da
Published: February 2024

Neste artigo, sugere-se um enfoque da cenografia digital, à luz de perspectivas animistas, na zona de contato entre cosmologias ameríndias, negro-africanas e afro-brasileiras, que, a partir de outras vivências e noções sobre ritmo e movimento, produzem relações comunicativas com a alteridade. Para isso, tecem-se considerações com as noções de ritmo, vibração, luz e som, segundo as conceituações apresentadas por Kaká Werá Jecupé e Amadou Hampâté Bâ. Adicionalmente, como objeto de reflexão em relação à cena expandida, trata da abordagem transmídia do coletivo Kawin, cujos procedimentos criativos investigam vivências rítmicas expandidas entre a dança, o som, as artes visuais e a cenografia digital. O estudo propõe, assim, uma abordagem não normativa da cenografia digital em sua interação com a performance.
The Correspondence of Fr Matthew Gaughren OMI (1888-1890)
Authors: Murray Edmundo , Walsh Edward
Published: February 2024

In mid-1888, Fr Matthew Gaughren (1843-1914) was sent to Argentina by his superior, the O.M.I. provincial in Great Britain, on a “begging expedition”, which aimed at collecting money among the Irish settlers to lessen the debt upon the church of Our Lady of Grace at Tower Hill. However, Gaughren changed the priorities of his mission in South America and appealed to the English-speaking community to support the Irish immigrants who arrived in Buenos Aires in February 1889 on the Dresden steamer ship from Cork and were sent to an ill-fated Irish Colony in Napostá, near the port of Bahía Blanca. His thinking and his struggle are revealed in the following letters, collected from various archival sources, which are now being published, most of them for the first time, in their complete form.
British Linguistic Colonialism in Ireland and India: A Comparison Between Brian Friel’s Translations and Contemporary Anglophone Indian Literature
Authors: Mondo Costanza
Published: February 2024

Ireland and India have a long-standing cultural heritage and also share similarities in certain colonial traits. This paper aims at analysing the phenomenon of linguistic colonialism – in this case the imposition of the English language – and its features by drawing a literary parallel between Ireland and India. Through the comparison of excerpts from Brian Friel’s Translations and passages from contemporary Anglophone Indian literature, this paper will investigate the similarities and differences between the experiences of these two former British colonies. While Friel’s play is set in nineteenth-century Donegal, some of the examples of contemporary Anglophone Indian literature that are provided stretch backwards to reach the nineteenth century, while others engage with contemporary times and the legacy of linguistic colonialism. The features of linguistic colonialism that I will examine are dealt with in three sections that focus on mapping and translation, the treatment of toponyms and names, and the relationship between school and language.
Woman Undone by Brokentalkers: Activism with a Difference
Authors: Young Helena
Published: February 2024

Brokentalkers theatre company first set up in 2001 may be described as a fearless, innovative organisation which has from the outset tried to balance the inequalities prevalent in Irish society. It comprises of Feidlim Cannon and Gary Keegan who describe their ethos as to devise original, accessible live performance and explore new forms that challenge traditional ideologies of text-based theatre. They use the postdramatic medium in order to convey the urgency of a particular situation and in line with this, their performances can often include slapstick, violent physical action, pop cultures, breaking of the illusion and hysterical outbursts from the actors. One of their more recent performances, Woman Undone, which premiered in 2018, is an impactful reimagining and reconstruction of an aspect of blues singer, Mary Coughlan’s life. This essay investigates the use of dramaturgical strategies such as musicality, bodily movement and cross gender casting in the performance in order to highlight the situation of those who have been abused in Ireland. The microcosm of one well known woman’s experience is brought to the macrocosm of society to educate and enlighten all women.