Differential expression of mRNA 3'-end isoforms in cervical and ovarian cancers.

Early diagnosis and therapeutic targeting are continuing challenges for gynecological cancers. Here, we focus on cancer transcriptomes and describe the differential expression of 3'UTR isoforms in patients using an algorithm to detect differential poly(A) site usage. We find primarily 3'UTR shortening cases in cervical cancers compared with the normal cervix.

Surgical mitral valve repair technique considerations based on the available evidence.

Mitral valve regurgitation is the second most common valve disease in the western world. Surgery is currently the best tool for generating a long-lasting elimination of mitral valve regurgitation. However, the mitral valve apparatus is a complex anatomical and functional structure, and repair results and durability show substantial heterogeneity.

Cardiac Surgery 2021 Reviewed.

PubMed displayed more than 35,000 hits for the search term "cardiac surgery AND 2021." We used the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-analyses) approach and selected relevant publications for a results-oriented summary. As in recent years, we reviewed the fields of coronary and conventional valve surgery and their overlap with their interventional alternatives.

Targeting HIF1-alpha/miR-326/ITGA5 axis potentiates chemotherapy response in triple-negative breast cancer.

Purpose: Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer that is frequently treated with chemotherapy. However, many patients exhibit either de novo chemoresistance or ultimately develop resistance to chemotherapy, leading to significantly high mortality rates. Therefore, increasing the efficacy of chemotherapy has potential to improve patient outcomes.

Slide type landslide susceptibility assessment of the Büyük Menderes watershed using artificial neural network method.

The Büyük Menderes watershed is the largest drainage watershed in Western Anatolia with an area of approximately 26,000 km. In the study area, almost 863 landslides occurred, extending over 222 km with a mean landslide area of 0.21 km.

Identification of an mRNA isoform switch for HNRNPA1 in breast cancers.

Roles of HNRNPA1 are beginning to emerge in cancers; however, mechanisms causing deregulation of HNRNPA1 function remain elusive. Here, we describe an isoform switch between the 3'-UTR isoforms of HNRNPA1 in breast cancers. We show that the dominantly expressed isoform in mammary tissue has a short half-life.

A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ-EIF2γ interactions.

Eukaryotic translation initiates upon recruitment of the EIF2-GTP·Met-tRNA ternary complex (TC) to the ribosomes. EIF2 (α, β, γ subunits) is a GTPase. The GDP to GTP exchange within EIF2 is facilitated by the guanine nucleotide exchange factor EIF2B (α-ε subunits).

A prelude to the proximity interaction mapping of CXXC5.

CXXC5 is a member of the zinc-finger CXXC family proteins that interact with unmodified CpG dinucleotides through a conserved ZF-CXXC domain. CXXC5 is involved in the modulation of gene expressions that lead to alterations in diverse cellular events. However, the underlying mechanism of CXXC5-modulated gene expressions remains unclear.

A CpG island promoter drives the CXXC5 gene expression.

CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown.

MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets.

Motivation: Next generation sequencing enabled the fast accumulation of genomic data at public repositories. This technology also made it possible to better understand the regulation of gene expression by transcription factors (TFs) and various chromatin-associated proteins through the integration of chromatin immunoprecipitation (ChIP-Seq). The Cistrome Project has become one of the indispensable research portals for biologists to access and analyze data generated with thousands of ChIP-Seq experiments.

OPCAB surgery with an alternative retraction method: a single-centre experience.

Background: The off-pump coronary artery bypass (OPCAB) technique, which is used in order to avoid the side effects of cardiopulmonary bypass, is often questioned in terms of its efficacy and safety. Also, in this technique, surgeon experience plays a very important role. In this study, we share the results of our 606 OPCAB cases with an alternative retraction technique.

JOA: Joint Overlap Analysis of multiple genomic interval sets.

Background: Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose restrictions such as not allowing nested intervals or requiring intervals to be sorted when finding overlaps in two or more interval sets.

A New Arterial Cannulation Technique: Arterial Cannulation through Aortic Anastomosis ("Kaplan" Technique).

We performed Bentall procedure on a 65-year-old male patient. Cardiopulmonary bypass was initiated via cannulation of the aneurysmatic segment of the aorta. Distal anastomosis was performed with the open technique under deep hypothermic circulatory arrest at 18°C.

Open Heart Surgery at Patient's Own Temperature Without Active Cooling.

Background: Hypothermia is a method of myocardial protection in cardiac surgery. This protection occurs by decreasing the metabolic demands, however, it creates susceptibility to various problems. In this study, we investigated patients operated on under normothermia (at the patient's own temperature) and hypothermia for postoperative differences.

An aortic valve papillary fibroelastoma: A case report.

Papillary fibroelastomas are rare tumors of the heart, mostly involving the valves. They can be asymptomatic and diagnosed incidentally or they can cause life-threatening clinic scenarios including cerebrovascular accidents, coronary arterial occlusions, or peripheral embolisms. Papillary fibroelastomas can be easily excised surgically using valve sparing techniques with low complication rates and without recurrence.

Open Cardiac Surgery without Blood and Blood Products Transplantation.

Background: Blood transfusions are the most common type of tissue and organ transplantation. Perioperative and postoperative transfusions may cause morbidity and mortality and transfusion should based on only hematocrit values but also on hemodynamic and clinical parameters of the patient, which cannot be ignored.

Methods: A prospective study was conducted between January 2015 and October 2016 with adult patients undergoing elective open heart surgery.

A multiplex primer design algorithm for target amplification of continuous genomic regions.

Background: Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing.

Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer.

Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. Therefore, we propose a pipeline to uncover patterns of alternative polyadenylation (APA), a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we analyzed expression data for 1045 cancer patients and found a significant shift in usage of poly(A) signals in common tumor types (breast, colon, lung, prostate, gastric, and ovarian) compared to normal tissues.

Comparison of tissue/disease specific integrated networks using directed graphlet signatures.

Background: Analysis of integrated genome-scale networks is a challenging problem due to heterogeneity of high-throughput data. There are several topological measures, such as graphlet counts, for characterization of biological networks.

Results: In this paper, we present methods for counting small sub-graph patterns in integrated genome-scale networks which are modeled as labeled multidigraphs.

Stent Embolism after Coronary Angiography: Case Report.

Endovascular interventions are widely performed of late; complications including stent embolism of arteries and veins, dislocation, or malposition of medical devices are frequently seen. Peripheral stent embolisms are generally asymptomatic, but when they cause acute ischemia or severe symptoms like claudication they must be removed. Stents can be removed not only with surgical techniques but also with endovascular maneuvers.

SUMONA: A supervised method for optimizing network alignment.

This study focuses on improving the multi-objective memetic algorithm for protein-protein interaction (PPI) network alignment, Optimizing Network Aligner - OptNetAlign, via integration with other existing network alignment methods such as SPINAL, NETAL and HubAlign. The output of this algorithm is an elite set of aligned networks all of which are optimal with respect to multiple user-defined criteria. However, OptNetAlign is an unsupervised genetic algorithm that initiates its search with completely random solutions and it requires substantial running times to generate an elite set of solutions that have high scores with respect to the given criteria.

Alternative Polyadenylation: Another Foe in Cancer.

Advancements in sequencing and transcriptome analysis methods have led to seminal discoveries that have begun to unravel the complexity of cancer. These studies are paving the way toward the development of improved diagnostics, prognostic predictions, and targeted treatment options. However, it is clear that pieces of the cancer puzzle are still missing.

3'UTR shortening and EGF signaling: implications for breast cancer.

Alternative polyadenylation (APA) plays a role in gene expression regulation generally by shortening of 3'UTRs (untranslated regions) upon proliferative signals and relieving microRNA-mediated repression. Owing to high proliferative indices of triple negative breast cancers (TNBCs), we hypothesized APA to cause 3'UTR length changes in this aggressive subgroup of breast cancers. Our probe-based meta-analysis approach identified 3'UTR length alterations where the significant majority was shortening events (∼70%, 113 of 165) of mostly proliferation-related transcripts in 520 TNBC patients compared with controls.

Open distal anastomosis technique for ascending aortic aneurysm repair without cerebral perfusion.

Background: This study aimed to report the outcomes of patients who underwent proximal thoracic aortic aneurysm surgery with open distal anastomosis technique but without cerebral perfusion, instead under deep hypothermic circulatory arrest.

Methods: Thirty patients (21 male, 9 female) who underwent ascending aortic aneurysm repair with open distal anastomosis technique were included. The average age was 60.

Reconstruction of the temporal signaling network in Salmonella-infected human cells.

Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the host proteins. Given that the bacterial infection modifies the response network of the host, a more coherent view of the underlying biological processes and the signaling networks can be obtained by using a network modeling approach based on the reverse engineering principles.