bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcriptional activity profile of inhibitor apoptosis protein encoding genes in colon cancer patients
Authors: Waniczek Dariusz , Nowak Marcin , Lorenc-Góra Justyna , Muc-Wierzgoń Małgorzata , Mazurek Urszula , Bichalska-Lach Magda , Lorenc Zbigniew 
Published: November 2021

Abstract
The inhibitor of apoptosis family proteins (IAPs) plays a crucial role in the process of carcinogenesis by regulating apoptosis and maintaining the tissue balance.
In this study, a transcriptomic analysis of IAP-encoding genes in colon cancer was performed using oligonucleotide microarrays.
Adenocarcinoma and healthy colon tissue samples were collected from 32 patients (16 females and 16 males) who underwent surgery due to colon cancer. The mRNA was extracted from tissue samples and tested using oligonucleotide microarrays (Affymetrix). The results were validated using the qRT-PCR technique. Hierarchical grouping was used to allocate 37 samples of normalized mRNA concentrations into 4 groups, with statistically significant differences in gene expression between these groups. The group of genes associated with colon cancer, including IAP-encoding gene - BIRC5 (Survivin), was selected for further testing.
Our study confirmed an increased expression of BIRC5 in colon cancer tissue when compared to the control group. Increased levels of Neuronal Apoptosis Inhibitory Proteins were detected only in low-stage colon cancer, while the expression of Human X Chromosome-Encoded inhibitor of apoptosis family proteins decreased in colon cancer.
The transcriptional activity of IAP-encoding genes varied, depending on the severity of colon cancer. The concentration of mRNA, encoding BIRC5 was elevated in samples obtained from more advanced colon cancer. Hence BIRC5 could be used as a complementary parameter for the diagnosis and prognosis of colon cancer.
Familial adenomatous polyposis associated with desmoid tumors presenting with abdominal abscess
Authors: Liu Ailing , Liu Hua , Ding Xueli , Wu Jun , Tian Zibin , Mao Tao 
Published: November 2021

Abstract

Rationale:
Familial adenomatous polyposis (FAP) associated with desmoids tumors (DTs) complicated by abscess formation is rare. The management is not easy and the choice of the best treatment may be controversial.

Patient concerns:
A 33-year-old man was admitted to our hospital for abdominal pain, fever, chills, nausea, and vomiting. He had a family history of FAP, and history of abdominal surgery.

Diagnoses:
An abdominal enhanced chest computed tomography (CT) scan revealed a soft tissue mass in the abdominal wall and an irregular mesenteric soft tissue mass with internal fistula and intra-abdominal abscess. A CT-guided biopsy of the abdominal wall mass revealed DTs.

Interventions:
The patient was given oral antibiotics for 6 months, and ultimately underwent surgery.

Outcomes:
The patient had no evidence of recurrence on follow-up at 10 months.

Lessons:
This case indicates that for patients with FAP who have a history of abdominal surgery and a progressively enlarging mass and abscess in the abdomen, it is necessary to consider the possibility of DTs. FAP-related DTs are rarely complicated by abscess formation. Antibiotic therapy plus surgical resection of the tumor may be effective and make good prognosis.
Limb-salvage surgery using personalized 3D-printed porous tantalum prosthesis for distal radial osteosarcoma
Authors: Chen Ge , Yin Yiran , Chen Chang 
Published: November 2021

Abstract

Rationale:
Three-dimensional (3D) printing has been widely utilized for treating the tumors of bone and soft tissue. We herewith report a unique case of distal radial osteosarcoma who was treated with a 3D printed porous tantalum prosthesis.
Patient concerns: A 58-year-old Chinese male patient presented to our clinic complaining about a 6-month history of a progressive pain at his right hand, associated with a growing lump 2 months later.

Diagnosis:
Osteosarcoma of distal radius confirmed by percutaneous biopsy and tumor biopsy.

Interventions:
A limb-salvage surgery was performed with a 3D printed porous tantalum prosthesis, combined with the postoperative chemotherapy for 4 cycles.

Outcomes:
At 2-year follow-up, complete pain relief and satisfactory functional recovery of his right wrist were observed.

Lessons:
Personalized 3D printed prosthesis is an effective and feasible method for treating the osteosarcoma and reconstruction of complex bone defects.
Clinical outcomes in acute pancreatitis with relative bradycardia at fever onset
Authors: Okamoto Takeshi , Arashiyama Makoto , Nakamura Kenji , Tsugitomi Ryosuke , Fukuda Katsuyuki 
Published: November 2021

Abstract
While some acute pancreatitis (AP) patents with fever do not exhibit a corresponding increase in heart rate, the clinical significance of this phenomenon has not been studied. We investigated the clinical relevance of relative bradycardia (RB) in febrile AP.
A retrospective electronic chart review was conducted on consecutive patients admitted for AP at a tertiary referral center in Japan from January 1, 2010, to May 31, 2018. Presence of RB was determined at the first instance of fever, based on formulas used in previous studies.
Fever at or during admission was observed in 115 patients, of which 33% had RB. Fever was observed at presentation in 48% and within 48 hours in 94% of cases. Etiologies were alcoholic in 48% and gallstones in 17% of cases. RB patients were older (median age: 62 vs 51 years, P = .028) but had shorter median postfever lengths of stay (8 vs 12 days, P = .003), lower median Ranson scores (1 vs 2, P < .001), and were less likely to develop delirium (11% vs 38%, P = .002). Nineteen of 21 severe AP cases based on the Ranson score were nonbradycardia (P = .011). RB was also associated with lower white blood cell count, C-reactive protein, and lactate levels. On computed tomography, necrosis (P = .028) and moderate or severe pancreatitis (P = .041) were less frequently observed in patients with RB. There was a significant inverse correlation between RB and the Ranson score (−.305, P = .001). While RB was an independent predictors of postfever length of stay (LOS) in multiple regression analysis when the Ranson score was excluded (P = .010), it ceased to be significant when the Ranson score was included (P = .141).
AP patients with RB at fever onset had milder disease and shorter LOS compared to those with higher heart rates at fever onset. RB may be useful as a simple, early predictor of shorter LOS before the Ranson score can be calculated.
Prognostic markers compared to CD3+TIL in locally advanced nasopharyngeal carcinoma
Authors: Al-Rajhi Nasser , Mohammed Shamayel F. , Khoja Hatim A. , Al-Dehaim Mohammad , Ghebeh Hazem 
Published: November 2021

Abstract
Locally advanced nasopharyngeal carcinoma (LA-NPC) is more prevalent in some geographic regions, including Saudi Arabia. Typically, Tumor-Node-Metastasis (TNM) staging is used in NPC. However, it is inadequate to assess the prognosis of LA-NPC.
Therefore, we analyzed and compared several previously reported prognostic factors in LA-NPC patients, retrospectively, including CD3+tumor-infiltrating lymphocytes (TIL) and peripheral blood hemoglobin, EBV DNA copy number, ratios of albumin-to-alkaline phosphatase ratio (AAPR), neutrophils, or platelets-to-lymphocytes (NLR, PLR). The studied cohort was 83 LA-NPC patients previously recruited for a randomized phase II trial with a different aim.
Univariate cox regression analysis showed no significant correlation between any of the tested variables with disease-free survival (DFS) or overall survival (OS) with the exception of low CD3+ TIL infiltration, which correlated significantly with DFS (HR = 6.7, P = <.001) and OS (HR = 9.1, P = .043). Similarly, in a validated multivariate cox regression analysis, only low CD3+ TIL correlated significantly with DFS (HR = 7.0, P < .001 for TIL) and OS (HR = 9.4, P = .040).
Among tested parameters, CD3+ TIL was the only independent prognostic marker for DFS and OS in LA-NPC patients treated with CCRT. This study supports the use of CD3+TIL, over other factors, as an independent prognostic factor in LA-NPC.
[Un]Forgetting History: Preparing Public Health Professionals to Address Structural Racism
Authors: Rosario Carrie , Al Amin Saif , Parker Cedric 
Published: November 2021

Context:
Structural racism, a fundamental cause of health inequities, must be dismantled to fulfill society's interest in ensuring conditions in which all people have opportunities conducive to health. Correspondingly, the Ten Essential Public Health Services center equity, and Council on Education for Public Health (CEPH) accreditation criteria require public health students to learn about racism. However, little guidance is provided to help faculty empower future generations of public health professionals to challenge it.

Program:
In response to the 2020 murders of George Floyd, Ahmaud Arbery, and Breonna Taylor, faculty at UNC Greensboro denounced racism and recommitted to anti-racist pedagogy and praxis. In this article, we discuss integrated ways a graduate-level public health assessment and planning course empowered students to name structural racism, understand how it operates, and collaborate for action.

Implementation:
Specifically, we highlight (1) our use of the book The Color of Law as means to understand racism as a structural intervention; (2) the Harvard Case Teaching Method as an organizing framework to make the classroom a critically engaged democratic setting; (3) change experts from local health and nonprofit organizations engaged in policy making to address social determinants and disparities resulting from structural racism (eg, housing, health care access, food insecurity); and (4) engagement with a minority-owned nonprofit to allow for practice applying knowledge and skills to address local inequities.

Discussion:
Our 4-pronged pedagogical approach provides an innovative, tangible example for other public health programs as they reflect upon academic institutions' unique power and role in addressing the public health crisis of structural racism.
The Power of Connections: AAP COVID-19 ECHO Accelerates Responses During a Public Health Emergency
Authors: Bernstein Henry H. , Calabrese Trisha , Corcoran Peter , Flint Laurence E. , Munoz Flor M. 
Published: November 2021

Context:
Pediatric providers across the United States have sought guidance on how to care for the nation's children during the uncertain historic times of the COVID-19 pandemic. The health care community has been challenged by the unprecedented burden of caring for patients when they have evolving guidelines and limited information about the effects of the virus on children.

Program:
In response, the American Academy of Pediatrics (AAP) rapidly launched a national initiative to increase child health professionals' knowledge, skills, and self-efficacy. This COVID-19 ECHO (Extension for Community Healthcare Outcomes) program created communities of learners among child health professionals and subject matter expert faculty using didactic and case-based presentations that foster an “all-teach, all-learn” approach.

Implementation:
The initial AAP COVID-19 ECHO program hosted more than 900 participants in 127 individual virtual sessions, with approximately 25 participants per session. The evolving nature of the pandemic necessitated dynamic and continuous bidirectional flow of concerns and information relevant to participants. Session topics were selected in a “just-in-time” fashion based on participant feedback from the prospective postsession surveys and faculty recommendations; speakers brought data and expert recommendations.

Evaluation:
To assess impact, the AAP used a mixed-methods approach to evaluate the program's effectiveness in meeting its educational objectives. The 2-phase evaluation collected quantitative and qualitative data through an integrated feedback structure that utilized prospective postsession and retrospective postprogram surveys, along with postprogram focus groups.

Discussion:
As the COVID-19 pandemic surges and another influenza season is upon us, the ECHO model is an effective strategy for facilitating bidirectional communication and education to build child health professionals' knowledge, skills, and self-efficacy during an unprecedented and ongoing public health emergency.

Key Points
The ECHO model is an effective strategy for health care organizations to facilitate bidirectional communication and education in building health professionals' clinical knowledge, skills, and self-efficacy during the unprecedented and ongoing public health emergency of the COVID-19 pandemic.
Transmission potential of vaccinated and unvaccinated persons infected with the SARS-CoV-2 Delta variant in a federal prison, July—August 2021
Authors: Salvatore Phillip P. , Lee Christine C. , Sleweon Sadia , McCormick David W. , Nicolae Lavinia , Knipe Kristen , Dixon Thomas , Banta Robert , Ogle Isaac , Young Cristen , Dusseau Charles , Salmonson Shawn , Ogden Charles , Godwin Eric , Ballom TeCora , Ross Tara , Wynn Nhien Tran , David Ebenezer , Bessey Theresa K. , Kim Gimin , Suppiah Suganthi , Tamin Azaibi , Harcourt Jennifer L. , Sheth Mili , Lowe Luis , Browne Hannah , Tate Jacqueline E. , Kirking Hannah L. , Hagan Liesl M. 
Published: November 2021

AbstractBackgroundThe extent to which vaccinated persons who become infected with SARS-CoV-2 contribute to transmission is unclear. During a SARS-CoV-2 Delta variant outbreak among incarcerated persons with high vaccination rates in a federal prison, we assessed markers of viral shedding in vaccinated and unvaccinated persons.MethodsConsenting incarcerated persons with confirmed SARS-CoV-2 infection provided mid-turbinate nasal specimens daily for 10 consecutive days and reported symptom data via questionnaire. Real-time reverse transcription-polymerase chain reaction (RT-PCR), viral whole genome sequencing, and viral culture was performed on these nasal specimens. Duration of RT-PCR positivity and viral culture positivity was assessed using survival analysis.ResultsA total of 978 specimens were provided by 95 participants, of whom 78 (82%) were fully vaccinated and 17 (18%) were not fully vaccinated. No significant differences were detected in duration of RT-PCR positivity among fully vaccinated participants (median: 13 days) versus those not fully vaccinated (median: 13 days; p=0.50), or in duration of culture positivity (medians: 5 days and 5 days; p=0.29). Among fully vaccinated participants, overall duration of culture positivity was shorter among Moderna vaccine recipients versus Pfizer (p=0.048) or Janssen (p=0.003) vaccine recipients.ConclusionsAs this field continues to develop, clinicians and public health practitioners should consider vaccinated persons who become infected with SARS-CoV-2 to be no less infectious than unvaccinated persons. These findings are critically important, especially in congregate settings where viral transmission can lead to large outbreaks.
Comparison of seven modelling algorithms for GABA-edited 1H-MRS
Authors: Craven Alexander R. , Bhattacharyya Pallab K. , Clarke William T. , Dydak Ulrike , Edden Richard A. E. , Ersland Lars , Mandal Pravat K. , Mikkelsen Mark , Murdoch James B. , Near Jamie , Rideaux Reuben , Shukla Deepika , Wang Min , Wilson Martin , Zöllner Helge , Hugdahl Kenneth , Oeltzschner Georg 
Published: November 2021

AbstractEdited MRS sequences are widely used for studying GABA in the human brain. Several algorithms are available for modelling these data, deriving metabolite concentration estimates through peak fitting or a linear combination of basis spectra. The present study compares seven such algorithms, using data obtained in a large multi-site study.GABA-edited (GABA+, TE = 68 ms MEGA-PRESS) data from 222 subjects at 20 sites were processed via a standardised pipeline, before modelling with FSL-MRS, Gannet, AMARES, QUEST, LCModel, Osprey and Tarquin, using standardised vendor-specific basis sets (for GE, Philips and Siemens) where appropriate.After referencing metabolite estimates (to water or creatine), systematic differences in scale were observed between datasets acquired on different vendors’ hardware, presenting across algorithms. Scale differences across algorithms were also observed.Using the correlation between metabolite estimates and voxel tissue fraction as a benchmark, most algorithms were found to be similarly effective in detecting differences in GABA+. An inter-class correlation across all algorithms showed single-rater consistency for GABA+ estimates of around 0.38, indicating moderate agreement. Upon inclusion of a basis set component explicitly modelling the macromolecule signal underlying the observed 3.0 ppm GABA peaks, single-rater consistency improved to 0.44. Correlation between discrete pairs of algorithms varied, and was concerningly weak in some cases.Our findings highlight the need for consensus on appropriate modelling parameters across different algorithms, and for detailed reporting of the parameters adopted in individual studies to ensure reproducibility and meaningful comparison of outcomes between different studies.HighlightsGABA-edited MRS data from 222 healthy adults across 20 research sites were analyzedData were modelled using seven different algorithms, yielding GABA+ and Glx estimatesModerate agreement was seen across all the tested algorithmsAdding a component to represent co-edited macromolecule signals improved concordanceBaseline modelling emerged as major factor differentiating outcomes
Biogenic action of Lactobacillus plantarum SBT2227 promotes sleep in Drosophila melanogaster
Authors: Ko Taro , Murakami Hiroki , Kamikouchi Azusa , Ishimoto Hiroshi 
Published: November 2021

SUMMARYLactic acid bacteria (LAB) influence multiple aspects of host brain function via the production of active metabolites in the gut, which is known as the pre/pro-biotic action. However, little is known about the biogenic effects of LAB on host brain function. Here, we reported that the Lactobacillus plantarum SBT2227 promoted sleep in Drosophila melanogaster. Administration of SBT2227 primarily increased the amount of sleep and decreased sleep latency at the beginning of night-time. The sleep-promoting effects of SBT2227 were independent of the existing gut flora. Furthermore, heat treatment or mechanical crushing of SBT2227 did not suppress the sleep-promoting effects, indicative of biogenic action. Transcriptome analysis, and RNAi mini-screening for gut-derived peptide hormones revealed the requirement of neuropeptide F, a homologue of the mammalian neuropeptide Y, for the action of SBT2227. These biogenic effects of SBT2227 on the host sleep provide new insights into the interaction between the brain and gut bacteria.
Sensitive identification of known and unknown protease activities by unsupervised linear motif deconvolution
Authors: Uzozie Anuli C. , Smith Theodore G. , Chen Siyuan , Lange Philipp F. 
Published: November 2021

AbstractThe cleavage-site specificities for many proteases are not well-understood, restricting the utility of supervised classification methods. We present an algorithm and web interface to overcome this limitation through the unsupervised detection of overrepresented patterns in protein sequence data, providing insight into the mixture of protease activities contributing to a complex system.Here, we apply the RObust LInear Motif Deconvolution (RoLiM) algorithm to confidently detect substrate cleavage patterns for SARS-CoV-2 Mpro protease in N terminome data of an infected human cell line. Using mass spectrometry-based peptide data from a case-control comparison of 341 primary urothelial bladder cancer cases and 110 controls, we identified distinct sequence motifs indicative of increased MMP activity in urine from cancer patients. Evaluation of N terminal peptides from patient plasma post-chemotherapy detected novel Granzyme B/Corin activity.RoLiM will enhance unbiased investigation of peptide sequences to establish the composition of known and uncharacterized protease activities in biological systems.
Erasure of Biologically Meaningful Signal by Unsupervised scRNAseq Batch-correction Methods
Authors: Tyler Scott R , Guccione Ernesto , Schadt Eric E 
Published: November 2021

AbstractSingle cell RNAseq (scRNAseq) batches range from technical-replicates to multi-tissue atlases, thus requiring robust batch-correction methods that operate effectively across this spectrum of between-batch similarity. Commonly employed benchmarks quantifyremovalof batch effects and preservation ofwithin-batchvariation, the preservation of biologically meaningful differencesbetweenbatches has been under-researched. Here, we address these gaps, quantifying batch effects at the level of cluster composition and along overlapping topologies through the introduction of two new measures. We discovered that standard approaches of scRNAseq batch-correction erase cell-type and cell-state variation in real-world biological datasets, single cell gene expression atlases, andin silicoexperiments. We highlight through examples showing that these issues may create the artefactual appearance of external validation/replication of findings. Our results demonstrate that either biological effects, if known, must be balanced between batches (like bulk-techniques), or technical effects that vary between batches must be explicitly modeled to prevent erasure of biological variation by unsupervised batch correction approaches.
Studies of parenchymal texture added to mammographic breast density and risk of breast cancer: a systematic review of the methods used in the literature
Authors: Anandarajah Akila , Chen Yongzhen , Colditz Graham A. , Hardi Angela , Stoll Carolyn , Jiang Shu 
Published: November 2021

AbstractThis systematic review aimed to assess the methods used to classify mammographic breast parenchymal features in relation to prediction of future breast cancer including the time from mammogram to diagnosis of breast cancer, and methods for the identification of texture features and selection of features for inclusion in analysis. The databases including Medline (Ovid) 1946-,Embase.com1947-, CINAHL Plus 1937-, Scopus 1823-, Cochrane Library (including CENTRAL), andClinicaltrials.gov. were searched through October 2021 to extract published articles in English describing the relationship of parenchymal texture features with risk of breast cancer. Twenty-eight articles published since 2016 were included in the final review. Of these, 7 assessed texture features from film mammograms images, 3 did not report details of the image used, and the others used full field mammograms from Hologic, GE and other manufacturers. The identification of parenchymal texture features varied from using a predefined list to machine-driven identification. Reduction in number of features chosen for analysis in relation to cancer incidence then varied across statistical approaches and machine learning methods. The variation in approach and number of features identified for inclusion in analysis precluded generating a quantitative summary or meta-analysis of the value of these to improve predicting risk of future breast cancers. This updated overview of the state of the art revealed research gaps; based on these, we provide recommendations for future studies using parenchymal features for mammogram images to make use of accumulating image data, and external validation of prediction models that extend to 5 and 10 years to guide clinical risk management. By following these recommendations, we expect to improve risk classification and risk prediction for women to tailor screening and prevention strategies to level of risk.