bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competencies for Code Review
Authors: Wurzel Gonçalves Pavlína , Calikli Gül , Serebrenik Alexander , Bacchelli Alberto 
Published: April 2023

Peer code review is a widely practiced software engineering process in which software developers collaboratively evaluate and improve source code quality. Whether developers can perform good reviews depends on whether they have sufficient competence and experience. However, the knowledge of what competencies developers need to execute code review is currently limited, thus hindering, for example, the creation of effective support tools and training strategies. To address this gap, we firstly identified 27 competencies relevant to performing code review through expert validation. Later, we conducted an online survey with 105 reviewers to rank these competencies along four dimensions: frequency of usage, importance, proficiency, and desire of reviewers to improve in that competency. The survey shows that technical competencies are considered essential to performing reviews and that respondents feel generally confident in their technical proficiency. Moreover, reviewers feel less confident in how to communicate clearly and give constructive feedback - competencies they consider like-wise an essential part of reviewing. Therefore, research and education should focus in more detail on how to support and develop reviewers' potential to communicate effectively during reviews. In the paper, we also discuss further implications for training, code review performance assessment, and reviewers of different experience level.
Data and materials: https://doi.org/10.5281/zenodo.7401313
Face Work: A Human-Centered Investigation into Facial Verification in Gig Work
Authors: Watkins Elizabeth Anne 
Published: April 2023

Through intensive research on datasets, benchmarks, and models, the computer-vision community has taken great strides to identify the societal biases intrinsic to these technologies. Less is known about the last mile of the computer-vision machine-learning pipeline: on-the-ground integration into the real world. In this paper, I analyze facial verification technology (FVT) through its use as account verification in ride-hail work. Using a sociotechnical framework combined with empirical qualitative research methods, including interviews and analysis of an online community of workers, this research is a deep dive into recognition technologies at the level of local practice. Findings reveal the high-stakes articulation labor demanded of workers to be recognized by these systems, including maintaining multiple mobile devices, repeatedly uploading requisite images, spending time and resources visiting customer-service centers, and making physical changes to their bodies and environments. These strategies constitute repairs to the failures of computer vision in dynamic environments and are required to successfully engage in the sociotechnical interaction protocols demanded by FVT. Drawing on Erving Goffman's terminology around social interaction rituals, I term these cognitive and behavioral negotiations "face work." Drivers' dynamic, responsive, and ad-hoc attempts to become machine-readable have significant implications for relations between identity and power in spaces of security and work, as well as for the integration of machine-learning systems into safety-critical infrastructures. Ultimately, this research emphasizes the crucial role of end users who create and maintain the conditions required for computer vision to produce judgment.
Tumor-Agnostic Precision Medicine from the AACR GENIE Database: Clinical Implications
Authors: Gouda Mohamed A. , Nelson Blessie E. , Buschhorn Lars , Wahida Adam , Subbiah Vivek 
Published: April 2023

Abstract
Biomarker-driven cancer therapy has revolutionized precision oncology. With a better understanding of tumor biology, tissue-agnostic targets have been characterized and explored, which ultimately led to therapeutics with pan-cancer efficacy. To date, five molecular biomarkers have obtained FDA tissue-agnostic approval for targeted therapies and immunotherapies. Those include BRAFV600E mutations, RET fusions, NTRK fusions, high tumor mutation burden (TMB), and deficient mismatch repair/high microsatellite instability (dMMR/MSI-High). Herein, we have used data from AACR project GENIE to explore the clinico-genomic landscape of these alterations. AACR GENIE is a publicly accessible registry of genomic data from multiple collaborating cancer centers. Current database (version 13.0) includes sequencing data of 168,423 samples collected from patients with different cancers. We were able to identify BRAFV600E, RET fusions, NTRK fusions, and high TMB in 2.9%, 1.6%, 1.5%, and 15.2% of pan-cancer samples, respectively. In this article, we describe the distribution of those tissue-agnostic targets among different cancer types. In addition, we summarize the current prospect on the biology of these alterations and evidence on approved drugs, including pembrolizumab, dostarilmab, larotrectinib, entrectinib, selpercatinib, and dabrafenib/trametinib combination.
Integrative Analysis of a Large Real-World Cohort of Small Cell Lung Cancer Identifies Distinct Genetic Subtypes and Insights into Histologic Transformation
Authors: Sivakumar Smruthy , Moore Jay A. , Montesion Meagan , Sharaf Radwa , Lin Douglas I. , Colón Caterina I. , Fleishmann Zoe , Ebot Ericka M. , Newberg Justin Y. , Mills Jennifer M. , Hegde Priti S. , Pan Quintin , Dowlati Afshin , Frampton Garrett M. , Sage Julien , Lovly Christine M. 
Published: April 2023

Abstract

Small cell lung cancer (SCLC) is a recalcitrant neuroendocrine carcinoma with dismal survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied. Here we provide an integrated analysis of 3,600 “real-world” SCLC cases. This large cohort allowed us to identify new recurrent alterations and genetic subtypes, including STK11-mutant tumors (1.7%) and TP53/RB1 wild-type tumors (5.5%), as well as rare cases that were human papillomavirus–positive. In our cohort, gene amplifications on 4q12 are associated with increased overall survival, whereas CCNE1 amplification is associated with decreased overall survival. We also identify more frequent alterations in the PTEN pathway in brain metastases. Finally, profiling cases of SCLC containing oncogenic drivers typically associated with NSCLC demonstrates that SCLC transformation may occur across multiple distinct molecular cohorts of NSCLC. These novel and unsuspected genetic features of SCLC may help personalize treatment approaches for this fatal form of cancer.

Significance:
Minimal changes in therapy and survival outcomes have occurred in SCLC for the past four decades. The identification of new genetic subtypes and novel recurrent mutations as well as an improved understanding of the mechanisms of transformation to SCLC from NSCLC may guide the development of personalized therapies for subsets of patients with SCLC.
This article is highlighted in the In This Issue feature, p. 1501
A Transcriptome-Based Precision Oncology Platform for Patient–Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies
Authors: Mundi Prabhjot S. , Dela Cruz Filemon S. , Grunn Adina , Diolaiti Daniel , Mauguen Audrey , Rainey Allison R. , Guillan Kristina , Siddiquee Armaan , You Daoqi , Realubit Ronald , Karan Charles , Ortiz Michael V. , Douglass Eugene F. , Accordino Melissa , Mistretta Suzanne , Brogan Frances , Bruce Jeffrey N. , Caescu Cristina I. , Carvajal Richard D. , Crew Katherine D. , Decastro Guarionex , Heaney Mark , Henick Brian S. , Hershman Dawn L. , Hou June Y. , Iwamoto Fabio M. , Jurcic Joseph G. , Kiran Ravi P. , Kluger Michael D. , Kreisl Teri , Lamanna Nicole , Lassman Andrew B. , Lim Emerson A. , Manji Gulam A. , McKhann Guy M. , McKiernan James M. , Neugut Alfred I. , Olive Kenneth P. , Rosenblat Todd , Schwartz Gary K. , Shu Catherine A. , Sisti Michael B. , Tergas Ana , Vattakalam Reena M. , Welch Mary , Wenske Sven , Wright Jason D. , Canoll Peter , Hibshoosh Hanina , Kalinsky Kevin , Aburi Mahalaxmi , Sims Peter A. , Alvarez Mariano J. , Kung Andrew L. , Califano Andrea 
Published: April 2023

Abstract

Predicting in vivo response to antineoplastics remains an elusive challenge. We performed a first-of-kind evaluation of two transcriptome-based precision cancer medicine methodologies to predict tumor sensitivity to a comprehensive repertoire of clinically relevant oncology drugs, whose mechanism of action we experimentally assessed in cognate cell lines. We enrolled patients with histologically distinct, poor-prognosis malignancies who had progressed on multiple therapies, and developed low-passage, patient-derived xenograft models that were used to validate 35 patient-specific drug predictions. Both OncoTarget, which identifies high-affinity inhibitors of individual master regulator (MR) proteins, and OncoTreat, which identifies drugs that invert the transcriptional activity of hyperconnected MR modules, produced highly significant 30-day disease control rates (68% and 91%, respectively). Moreover, of 18 OncoTreat-predicted drugs, 15 induced the predicted MR-module activity inversion in vivo. Predicted drugs significantly outperformed antineoplastic drugs selected as unpredicted controls, suggesting these methods may substantively complement existing precision cancer medicine approaches, as also illustrated by a case study.

Significance:
Complementary precision cancer medicine paradigms are needed to broaden the clinical benefit realized through genetic profiling and immunotherapy. In this first-in-class application, we introduce two transcriptome-based tumor-agnostic systems biology tools to predict drug response in vivo. OncoTarget and OncoTreat are scalable for the design of basket and umbrella clinical trials.
This article is highlighted in the In This Issue feature, p. 1275
High Expression of MHC Class I Overcomes Cancer Immunotherapy Resistance Due to IFNγ Signaling Pathway Defects
Authors: Kawase Katsushige , Kawashima Shusuke , Nagasaki Joji , Inozume Takashi , Tanji Etsuko , Kawazu Masahito , Hanazawa Toyoyuki , Togashi Yosuke 
Published: April 2023

Abstract
IFNγ signaling pathway defects are well-known mechanisms of resistance to immune checkpoint inhibitors. However, conflicting data have been reported, and the detailed mechanisms remain unclear. In this study, we have demonstrated that resistance to immune checkpoint inhibitors owing to IFNγ signaling pathway defects may be primarily caused by reduced MHC-I expression rather than by the loss of inhibitory effects on cellular proliferation or decreased chemokine production. In particular, we found that chemokines that recruit effector T cells were mainly produced by immune cells rather than cancer cells in the tumor microenvironment of a mouse model, with defects in IFNγ signaling pathways. Furthermore, we found a response to immune checkpoint inhibitors in a patient with JAK-negative head and neck squamous cell carcinoma whose HLA-I expression level was maintained. In addition, CRISPR screening to identify molecules associated with elevated MHC-I expression independent of IFNγ signaling pathways demonstrated that guanine nucleotide-binding protein subunit gamma 4 (GNG4) maintained MHC-I expression via the NF-κB signaling pathway. Our results indicate that patients with IFNγ signaling pathway defects are not always resistant to immune checkpoint inhibitors and highlight the importance of MHC-I expression among the pathways and the possibility of NF-κB–targeted therapies to overcome such resistance.
See related Spotlight by Haugh and Daud, p. 864
Projected Changes to Streamflow and Stream Temperature in Central Texas: How Much Will the River Flow?
Authors: Wootten Adrienne M. , Martin Elinor , Randklev Charles R. , Smith Ryan 
Published: April 2023

Abstract
Riverine ecosystems are dependent in large part on the climate of the region, and climate change is expected to alter climatic factors of interest, such as precipitation, temperature, and evapotranspiration. In central Texas, precipitation is expected to decrease while temperature increases as the climate changes. Drought and flooding events are also expected to increase in the region, which will also affect streamflow and stream temperature in riverine ecosystems. Numerous studies have assessed the potential impacts of climate change on riverine species. This study examines the projected climate changes, determines potential changes in streamflow and stream temperature for river basins in central Texas, and assesses the appropriate uses of climate projections for riverine species impact assessments, using the Texas fatmucket (Lampsilis bracteata) as a case study. Previously established regression methods were used to produce projections of streamflow and stream temperature. This study finds that streamflow is projected to decrease and stream temperature is projected to increase. Using thermal tolerance thresholds previously determined for the Lampsilis bracteata, this study also finds that the lethal temperature events for the Lampsilis bracteata will increase. This study makes several recommendations on the use of downscaled climate projections for impact assessments for riverine species such as the Lampsilis bracteata.
RPL21 interacts with LAMP3 to promote colorectal cancer invasion and metastasis by regulating focal adhesion formation
Authors: Zhu Jiaxian , Long Ting , Gao Lingfang , Zhong Yan , Wang Ping , Wang Xiaoyan , Li Zuguo , Hu Zhiyan 
Published: April 2023

Abstract
Background
Metastasis is the leading cause of death among patients with colorectal cancer (CRC). Therefore, it is important to explore the molecular mechanisms of metastasis to develop effective therapeutic targets for CRC. In the present study, ribosomal protein L21 (RPL21) was considered as being involved in promoting CRC metastasis, yet the underlying mechanism requires further investigation.

Methods
Immunohistochemistry, western blotting, and quantitative reverse transcription polymerase chain reaction were performed to measure the expression of RPL21 and lysosome-associated membrane protein 3 (LAMP3) in CRC tissues and cells. Wound healing, transwell migration, and invasion assays were performed to study the migration and invasion of cultured CRC cells. An orthotopic CRC mouse model was developed to investigate the metastatic ability of CRC. Transcriptome sequencing was conducted to identify the genes related to RPL21. The dual-luciferase reporter gene assay was performed to determine the transcriptional activity of transcription factor EB (TFEB). The GST/His pull-down assay was performed to investigate the specific binding sites of RPL21 and LAMP3. The cell adhesion assay was performed to determine the adhesion ability of CRC cells. Immunofluorescence staining was performed to observe focal adhesions (FAs).

Results
RPL21 was highly expressed in CRC, contributing to tumor invasiveness and poor patient prognosis. Functionally, RPL21 promoted the migration and invasion of CRC cells in vitro and tumor metastasis in vivo. Moreover, LAMP3 was identified as being highly related to RPL21 and was essential in promoting the migration and invasion of CRC cells. Mechanistically, RPL21 activated the transcriptional function of TFEB to upregulate LAMP3 expression. RPL21 directly bound to the aa 341–416 domain of LAMP3 via its aa 1–40 and aa 111–160 segments. The combination of RPL21 and LAMP3 enhanced the stability of the RPL21 protein by suppressing the degradation of the ubiquitin–proteasome system. Furthermore, RPL21 and LAMP3 promoted the formation of immature FAs by activating the FAK/paxillin/ERK signaling pathway.

Conclusions
RPL21 promoted invasion and metastasis by regulating FA formation in a LAMP3-dependent manner during CRC progression. The interaction between RPL21 and LAMP3 may function as a potential therapeutic target against CRC.
Powering Ghana’s future: unraveling the dynamics of electricity generation and the path to sustainable energy
Authors: Atuahene Sampson Agyapong , Sheng Qian Xu 
Published: April 2023

AbstractThis study investigates powering Ghana’s future: unraveling the dynamics of electricity generation and the path to sustainable energy by estimating endogenous parameters and employing an unrestricted Vector Autoregression (VAR) model. The model examines the linear lead–lag relationships between variables in the Ghanaian electricity sector and power consumption, using data from 2002 to 2021. The results reveal structural long-and-short-run headwinds for the unrestricted models and indicate that the growth rate of the Gross Domestic Product (GDP) and electricity from fossil fuels are directly correlated. Granger causality analysis highlights a feedback relationship between GDP growth rate and electricity from fossil fuel sources. The impulse response function reveals that the GDP growth rate is sensitive to exogenous shocks with lasting effects. Variance decomposition results show that renewable energy without hydropower explains a minimal variance due to shocks, while total global greenhouse emissions account for a significant proportion of the variance due to headwinds. Electricity from fossil fuel sources explains a substantial part of the variance due to headwinds, suggesting Ghana’s overreliance on conventional energy sources. The study forecasts that installed renewable energy capacity will experience considerable growth by 2036, accounting for most of the energy mix. To promote a sustainable energy future, the study recommends implementing fiscal instruments that incentivize renewable energy consumption, gradually diversifying the energy mix towards natural gas as a medium-term transition fuel for grid electricity generation and shifting entirely to renewables in the long time. This research contributes valuable insights into the dynamics of electricity generation in Ghana and provides policy recommendations for sustainable energy development.
PCK1 activates oncogenic autophagy via down-regulation Serine phosphorylation of UBAP2L and antagonizes colorectal cancer growth
Authors: Zhang Xiangyan , Tao Geru , Jiang Jie , Qu Tingting , Zhao Shuchao , Xu Ping , Zhao Ya’nan , Xing Xiaoming , Qin Shucun 
Published: April 2023

AbstractPhosphoenolpyruvate carboxykinase 1 (PCK1) is the rate-limiting enzyme in gluconeogenesis. PCK1 is considered an anti-oncogene in several human cancers. In this study, we aimed to determine the functions of PCK1 in colorectal cancer (CRC). PCK1 expression in CRC tissues was tested by western blot and immunohistochemistry analyses and associations of PCK1 level with clinicopathological characteristics and disease survival evaluated. Further, we studied the effect of PCK1 on CRC cell proliferation and the underlying mechanisms. Our results show that PCK1 is expressed at significantly lower levels in CRC than in control tissues. High PCK1 expression was correlated with smaller tumor diameter and less bowel wall invasion (T stage). Overexpression and knockdown experiments demonstrated that PCK1 inhibits CRC cell growth both in vitro and in vivo. Mechanistically, PCK1 antagonizes CRC growth via inactivating UBAP2L phosphorylation at serine 454 and enhancing autophagy. Overall, our findings reveal a novel molecular mechanism involving PCK1 and autophagy, and highlight PCK1 as a promising candidate therapeutic target in CRC.
CAFs-derived rho-associated kinase1 mediated EMT to promote laryngeal squamous cell carcinoma metastasis
Authors: Yang Liyun , Gong Shiqi , Qiao Peipei , Zhao Runyu , Huang Shuixian , Zhou Jieyu , Hu An 
Published: April 2023

Abstract
Background
Cancer-associated fibroblasts (CAFs) play an essential role in tumorigenesis and development of cancers. Nevertheless, the specific molecular mechanism of tumorigenesis and development in Laryngeal squamous cell carcinoma (LSCC) still unknown.

Methods
CAFs, CPFs and NFs were isolated and identified from laryngeal cancer, para-laryngeal cancer and normal tissues. Immunofluorescent staining, Rt-PCR and Western Blot were used to detect the expression of related proteins. Wound healing, migration, invasion and animal experiments were used to examine the ability of movement, migration, invasion and metastasis of LSCC.

Results
ROCK1, was highly expressed in CAFs and CAFs enhanced LSCC metastasis in vivo and vitro, and downregulation of ROCK1 in CAFs inhibited the migration and invasion of LSCC cells. While increasing ROCK1 expression in NFs promoted the migration and invasion of LSCC cells. Further studies revealed that epithelial-mesenchymal transition (EMT) and JAK2/STAT3/ERK1/2 pathway might play an essential role in promoting metastasis of LSCC. In addition, inhibition activity of ROCK1 or JAK2/STAT3/ERK1/2 signal molecules significantly reduced EMT and metastasis.

Conclusions
CAFs-derived ROCK1 via JAK2/STAT3/ERK1/2 axis mediated EMT to promote LSCC metastasis and targeting ROCK1 might provide a potential treatment strategy for LSCC.
Identification of mitochondrial respiratory chain signature for predicting prognosis and immunotherapy response in stomach adenocarcinoma
Authors: Yang Jing , Jin Feifan , Li Huanjuan , Shen Yuhuan , Shi Weilin , Wang Lina , Zhong Lei , Wu Gongqiang , Wu Qiaoliang , Li Yanchun 
Published: April 2023

AbstractStomach adenocarcinoma (STAD) is the third leading cause of cancer-related deaths and the fifth most prevalent malignancy worldwide. Mitochondrial respiratory chain complexes play a crucial role in STAD pathogenesis. However, how mitochondrial respiratory chain complex genes (MRCCGs) affect the prognosis and tumor microenvironment in STAD remains unclear. In this study, we systematically analyzed genetic alterations and copy number variations of different expression densities of MRCCGs, based on 806 samples from two independent STAD cohorts. Then we employed the unsupervised clustering method to classify the samples into three expression patterns based on the prognostic MRCCG expressions, and found that they were involved in different biological pathways and correlated with the clinicopathological characteristics, immune cell infiltration, and prognosis of STAD. Subsequently, we conducted a univariate Cox regression analysis to identify the prognostic value of 1175 subtype-related differentially expressed genes (DEGs) and screened out 555 prognostic-related genes. Principal component analysis was performed and developed the MG score system to quantify MRCCG patterns of STAD. The prognostic significance of MG Score was validated in three cohorts. The low MG score group, characterized by increased microsatellite instability-high (MSI-H), tumor mutation burden (TMB), PD-L1 expression, had a better prognosis. Interestingly, we demonstrated MRCCG patterns score could predict the sensitivity to ferroptosis inducing therapy. Our comprehensive analysis of MRCCGs in STAD demonstrated their potential roles in the tumor-immune-stromal microenvironment, clinicopathological features, and prognosis. Our findings highlight that MRCCGs may provide a new understanding of immunotherapy strategies for gastric cancer and provide a new perspective on the development of personalized immune therapeutic strategies for patients with STAD.