gebhart/patrepeval huggingface dataset:
Data from Very Long-term Survival Following Resection for Pancreatic Cancer Is Not Explained by Commonly Mutated Genes: Results of Whole-Exome Sequencing Analysis (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The median survival following surgical resection of pancreatic ductal adenocarcinoma (PDAC) is currently &lt;20 months. However, survival ≥10 years is achieved by a small subset of patients who are defined as very long-term survivors (VLTS). The goal of this study was to determine whether specific genetic alterations in resected PDACs determined very long-term survival.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; We sequenced the exomes of eight PDACs from patients who survived ≥10 years. On the basis of the results of the exomic analysis, targeted sequencing of selected genes was performed in a series of 27 additional PDACs from VLTSs.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; &lt;i&gt;KRAS&lt;/i&gt; mutations were identified in 33 of 35 cancers (94%) from VLTSs and represented the most prevalent alteration in our cohort. &lt;i&gt;TP53&lt;/i&gt;, &lt;i&gt;SMAD4&lt;/i&gt;, and &lt;i&gt;CDKN2A&lt;/i&gt; mutations occurred in 69%, 26%, and 17%, respectively. Mutations in &lt;i&gt;RNF43&lt;/i&gt;, which have been previously associated with intraductal papillary mucinous neoplasms, were identified in four of the 35 cancers (11%). Taken together, our data show no difference in somatic mutations in carcinomas from VLTSs compared with available data from PDACs unselected for survival. Comparison of clinicopathologic features between VLTSs and a matching control group demonstrated that younger age, earlier stage, well/moderate grade of differentiation, and negative resection margins were associated with VLTS. However, more advanced stage, poor grade, or nodal disease did not preclude long-term survival.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our results suggest that in most patients, somatic mutations in commonly mutated genes are unlikely to be the primary determinant of very long-term survival following surgical resection of PDAC. &lt;i&gt;Clin Cancer Res; 21(8); 1944–50. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Transcriptional repression of plasma cell differentiation is orchestrated by aberrant over-expression of the ETS factorSPIBin Waldenström macroglobulinaemia (2014)

In Waldenström macroglobulinaemia (WM), the mechanism(s) responsible for repression of B-cell differentiation remains unknown. We found that expression of SPIB and ID2 were significantly increased and decreased, respectively, in WM lymphoplasmacytic cells (LPC). Ectopic expression of SPIB in healthy donor CD19(+) cells inhibited plasmacytic differentiation in conjunction with decreased transcription of IRF4 and XBP1 spliced form. In primary WM LPC, knock-down of SPIB induced plasmacytic differentiation in conjunction with increased transcription of PRDM1, XBP1 spliced form, IRF4 and ID2. Knock-down of SPIB also led to decreased BCL2 expression. Given that SPIB is a direct target of POU2AF1 (OBF1) in complex with POU2F2 or POU2F1, we next examined their expression in WM LPC. POU2F2 transcription, as well as POU2F2 and POU2AF1 protein expression was higher in WM LPC. Ectopic expression of POU2F2 in healthy donor CD19(+) cells induced transcription of SPIB and suppressed transcription of PRDM1 and IRF4. Chromatin immunoprecipitation analysis in BCWM.1 WM cells confirmed binding of POU2F2 and POU2AF1 in SPIB and ID2 promoters. These findings establish a molecular hierarchy among POU2F2, SPIB and ID2 during B-cell differentiation, and suggest that aberrant expression of these transcription factors plays an important role in arresting plasmacytic differentiation in WM.
Initiation of Renal Replacement Therapy in the Intensive Care Unit in Vicenza (IRRIV) Score (2015)

We have developed a simple Score (IRRIV Score) to identify patients at high risk of requiring RRT. This score may serve as a standardized definition of the timing of initiation of RRT.
Mechanical Properties of Acoustically Levitated Granular Rafts (2022)

We investigate a model system for the rotational dynamics of inertial many-particle clustering, in which submillimeter objects are acoustically levitated in air. Driven by scattered sound, levitated grains selfassemble into a monolayer of particles, forming mesoscopic granular rafts with both an acoustic binding energy and a bending rigidity. Detuning the acoustic trap can give rise to stochastic forces and torques that impart angular momentum to levitated objects. As the angular momentum of a quasi-two-dimensional granular raft is increased, the raft deforms from a disk to an ellipse, eventually pinching off into multiple separate rafts, in a mechanism that resembles the breakup of a liquid drop. We extract the raft effective surface tension and elastic modulus and show that nonpairwise acoustic forces give rise to effective elastic moduli that scale with the raft size. We also show that the raft size controls the microstructural basis of plastic deformation, resulting in a transition from fracture to ductile failure.
Quantum Systems on Non-$k$-Hyperfinite Complexes: A Generalization of Classical Statistical Mechanics on Expander Graphs (2013)

We construct families of cell complexes that generalize expander graphs. These families are called non-$k$-hyperfinite, generalizing the idea of a non-hyperfinite (NH) family of graphs. Roughly speaking, such a complex has the property that one cannot remove a small fraction of points and be left with an object that looks $k-1$-dimensional at large scales. We then consider certain quantum systems on these complexes. A future goal is to construct a family of Hamiltonians such that every low energy state has topological order as part of an attempt to prove the quantum PCP conjecture. This goal is approached by constructing a toric code Hamiltonian with the property that every low energy state without vertex defects has topological order, a property that would not hold for any local system in any lattice $Z^d$ or indeed on any 1-hyperfinite complex. Further, such NH complexes find application in quantum coding theory. The hypergraph product codes[1] of Tillich and Zémor are generalized using NH complexes.
Federal guidelines on diagnosis and treatment of community-acquired pneumonia (2022)

Community-acquired pneumonia is one of the most common acute infectious diseases that has a significant share in the structure of mortality from respiratory diseases. It is extremely important to select rational antibiotic therapy which ensures optimal clinical efficacy, improved outcome, reduced rate of antibiotic resistance selection, and minimization of side effects. Methods . The target audience of these clinical recommendations are therapists, general practitioners, pulmonologists, anesthesiologist-resuscitators, and clinical pharmacologists. Each thesis-recommendation about diagnostic and therapeutic procedures has been scored according to the scale of classes of recommendations from 1 to 5 and A, B, C scale of the levels of evidence. The clinical recommendations also contain comments and explanations to these theses, algorithms for the diagnosis and treatment, and reference materials on the use of antibacterial drugs and microbiological (culture) tests. Conclusion . The presented clinical guidelines cover current information about the etiology, clinical manifestations, diagnosis and treatment tactics for community-acquired pneumonia. The presented clinical guidelines have been approved by the Scientific and Practical Council of the Ministry of Health of the Russian Federation in 2021.
Regulation of Mitochondrial Genome Inheritance by Autophagy and Ubiquitin-Proteasome System: Implications for Health, Fitness, and Fertility (2014)

Mitochondria, the energy-generating organelles, play a role in numerous cellular functions including adenosine triphosphate (ATP) production, cellular homeostasis, and apoptosis. Maternal inheritance of mitochondria and mitochondrial DNA (mtDNA) is universally observed in humans and most animals. In general, high levels of mitochondrial heteroplasmy might contribute to a detrimental effect on fitness and disease resistance. Therefore, a disposal of the sperm-derived mitochondria inside fertilized oocytes assures normal preimplantation embryo development. Here we summarize the current research and knowledge concerning the role of autophagic pathway and ubiquitin-proteasome-dependent proteolysis in sperm mitophagy in mammals, including humans. Current data indicate that sperm mitophagy inside the fertilized oocyte could occur along multiple degradation routes converging on autophagic clearance of paternal mitochondria. The influence of assisted reproductive therapies (ART) such as intracytoplasmic sperm injection (ICSI), mitochondrial replacement (MR), and assisted fertilization of oocytes from patients of advanced reproductive age on mitochondrial function, inheritance, and fitness and for the development and health of ART babies will be of particular interest to clinical audiences. Altogether, the study of sperm mitophagy after fertilization has implications in the timing of evolution and developmental and reproductive biology and in human health, fitness, and management of mitochondrial disease.
Health‐related quality of life in patients with melanoma – characterization of a Swedish cohort (2019)

Only few studies that have investigated the Health-Related Quality of Life (HR-QoL) in melanoma patients 1-4 , reviewed in Chernyshov et al.5 . This is to the best of our knowledge the first popula ...
Intra-embryo Gene Cassette Knockin by CRISPR/Cas9-Mediated Genome Editing with Adeno-Associated Viral Vector (2018)

Intra-embryo genome editing by CRISPR/Cas9 enables easy generation of gene-modified animals by non-homologous end joining (NHEJ)-mediated frameshift mutations or homology-directed repair (HDR)-mediated point mutations. However, large modifications, such as gene replacement or gene fusions, are still difficult to introduce in embryos without costly micromanipulators. Moreover, micromanipulation techniques for intra-embryo genome editing have been established in only a small set of animals. To overcome these issues, we developed a method of large-fragment DNA knockin without micromanipulation. In this study, we successfully delivered the knockin donor DNA into zygotes by adeno-associated virus (AAV) without removing the zona pellucida, and we succeeded in both large-DNA fragment knockin and whole exon exchange with electroporation of CRISPR/Cas9 ribonucleoprotein. By this method, we can exchange large DNA fragments conveniently in various animal species without micromanipulation.
Supramolecular Route to Fluorinated Coatings: Self-Assembly Between Poly(4-vinylpyridines) and Haloperfluorocarbons (2002)

A simple supramolecular method for the direct self-assembly of comb-like complexes composed of hydrocarbon polymers and perfluorocarbon mesogens is described. Halogen bonding is highly directional, so that perfluoroalkyl residues with their rigid rod-like architecture result in materials with a beautiful comb-like structure. The Figure shows an ORTEP view of such co-crystals.
Synthesis, Structure, and Electroluminescence of BR2q (R = Et, Ph, 2-Naphthyl and q = 8-Hydroxyquinolato) (1999)

Three 8-hydroxyquinolato (q) boron compounds B(C2H5)2q (1), BPh2q (2), and B(2-naph)2q (3) have been synthesized by the reaction of 8-hydroxyquinoline with an appropriate BR3 compound. Compounds 1−3 have a tetrahedral geometry as demonstrated by the structure of 1 determined by a single-crystal X-ray diffraction analysis. Compounds 1−3 emit a green-blue color at λmax = 495−500 nm when irradiated by UV light. The electroluminescent (EL) properties of 2 and 3 were examined by fabricating EL devices using 2 and 3 as the light-emitting layer, respectively. The devices of 2 produce a yellow-green light with broad emission spectra, attributed to the formation of an exciplex of 2 with the N,N‘-di-1-naphthyl-N,N‘-diphenylbenzidine (NPB) in the hole transport layer while the intrinsic EL emission of compound 3 was observed. Both 2 and 3 were found to be good electron transport materials in EL devices.
Asymmetric Aziridination of Cyclic Enones Using Chiral Diamine Catalysts and Its Application to the Total Synthesis of (−)-Agelastatin A (2011)

The asymmetric aziridination of cyclic enones with N-tosyloxycarbamates, using N-neopentyl 1,2-diphenylethylenediamine as a catalyst, and its application to the formal total synthesis of (-)-agelastatin A, using a one-pot silylation-selenylation procedure and the regioselective aziridine-opening by an azide anion as key steps, are described.
Hexagonal-Shaped Broadband Compact Scrimp Horn Antenna for Operation in $C$-Band (2012)

The performance of compact linearly polarized Short Circular Ring-loaded horn with Minimized cross-Polarization (Scrimp) horns with different aperture sizes is first evaluated using an in-house finite-difference time-domain (FDTD) computer-aided design (CAD) tool. Then, a very short hexagonal Scrimp horn with an aperture size of 1.5λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> is designed in <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</i> -band; its height is only 1.26λ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> . The experimental results demonstrate that the aperture efficiency is higher than 80% with a reflection coefficient lower than -17 dB over a 12.6% frequency bandwidth. Radiation patterns of excellent quality are measured with a cross-polarization level lower than - 28 dB over the entire bandwidth. These antennas are very attractive candidates for high-power focal array configurations in multifeed systems.
[Villonodular synovitis of the knee. Analysis of a series of 17 cases and review of the literature]. (1998)

Arthroscopy is the treatment of choice for localized forms. We propose a mixed concept with an anterior and parameniscal arthroscopic synovectomy (without meniscectomy), an open synovectomy for the posterior localization, and an open anterior synovectomy when the tumor mass is too voluminous.
Characterizing and predicting which bugs get fixed (2010)

We performed an empirical study to characterize factors that affect which bugs get fixed in Windows Vista and Windows 7, focusing on factors related to bug report edits and relationships between people involved in handling the bug. We found that bugs reported by people with better reputations were more likely to get fixed, as were bugs handled by people on the same team and working in geographical proximity. We reinforce these quantitative results with survey feedback from 358 Microsoft employees who were involved in Windows bugs. Survey respondents also mentioned additional qualitative influences on bug fixing, such as the importance of seniority and interpersonal skills of the bug reporter.
Associations of Cigarette Smoking and Alcohol Consumption With Advanced or Multiple Colorectal Adenoma Risks: A Colonoscopy-based Case-Control Study in Korea (2011)

The associations between alcohol consumption and cigarette smoking habits and the risk for colorectal adenomatous polyps according to the detailed clinical information about polyps were assessed in a large colonoscopy-based study. The study enrolled participants who visited the National Cancer Center of the Republic of Korea for cancer screening between April 2007 and April 2009. In 1,242 newly diagnosed colorectal adenoma patients and 3,019 polyp-free controls, past smokers (odds ratio (OR) = 1.31, 95% confidence interval (CI): 1.04, 1.65) and current smokers (OR = 1.70, 95% CI: 1.37, 2.11) had increased risks for adenomas compared with nonsmokers. Cigarette smoking conferred an even higher risk for advanced adenomas and 3 or more adenomas than for low-risk adenomas or a single adenoma. Dose-response relations were observed among the daily number of cigarettes smoked, the duration of smoking, the pack-years of smoking, and the risk for adenomas. A longer duration of alcohol consumption was associated with a higher risk for advanced adenomas (for >28 years of consumption: OR = 2.0, 95% CI: 1.10, 3.64) and 3 or more adenomas (OR = 2.19, 95% CI: 1.27, 3.76). In conclusion, cigarette smoking and alcohol consumption play roles in colorectal carcinogenesis, and the association differs by the clinical features of the adenomas.
Generation of apodized X-ray illumination and its application to scanning and diffraction microscopy (2016)

X-ray science has greatly benefited from the progress in X-ray optics. Advances in the design and the manufacturing techniques of X-ray optics are key to the success of various microscopic and spectroscopic techniques practiced today. Here the generation of apodized X-ray illumination using a two-stage deformable Kirkpatrick-Baez mirror system is presented. Such apodized illumination is marked by the suppression of the side-lobe intensities of the focused beam. Thus generated apodized illumination was employed to improve the image quality in scanning X-ray fluorescence microscopy. Imaging of a non-isolated object by coherent X-ray diffractive imaging with apodized illumination in a non-scanning mode is also presented.
The effects of iloprost infusion on microcirculation is independent of nitric oxide metabolites and endothelin‐1 in chronic peripheral ischaemia (1999)

This study provides evidence that iloprost enhances the microvascular functional capacity and clinical benefit for patients. The effects of the drug seem to be independently or not directly correlated with its interactions with vascular tone modulators such as NO2-/NO3- or ET-1.
337-OR: Hyperglycemia Lowers Lactate Clearance during Exercise in Type 1 Diabetes (2023)

To determine the role of hyperglycemia on lactate metabolism during exercise in type 1 diabetes (T1D), we studied 7 T1D participants during two visits (EuLoI; euglycemia, low insulin; HyLoI: hyperglycemia, low insulin) in random order. 7 nondiabetic (ND) subjects were studied on one occasion (EuLoI). Lactate turnover was measured using [1-13C] lactate before, during and after 60 min of exercise at 65% VO2 max. While lactate clearance was lower (p=0.031) during exercise at HyLoI than EuLoI in T1D, it was not different between T1D and ND subjects at EuLoI (p=0.707). In contrast, rate of lactate appearance during exercise was not different between EuLoI vs. HyLoI in T1D (p=0.129), demonstrating that higher plasma lactate concentration during exercise in HyLoI (p&amp;lt;0.001) was due to reduced lactate clearance in T1D. The results from this pilot study indicates that hyperglycemia modulates lactate metabolism during exercise by lowering lactate clearance in T1D individuals. This novel observation implies that exercise during hyperglycemia can lead to higher circulating lactate concentrations thus increasing the likelihood of reaching the lactate threshold sooner, in type 1 diabetes. Disclosure D.Romeres: None. Y.Yadav: None. F.Ruchi: None. R.Carter: None. C.Cobelli: None. R.Basu: Consultant; Sparrow Pharmaceuticals Inc, Research Support; Abbott Diabetes, AstraZeneca. A.Basu: None. Funding National Institutes of Health (DK29953 to R.B.), (DK85516 to A.B.)
Structural and functional diversity of microcins, gene-encoded antibacterial peptides from Enterobacteriaceae (2006)

Microcins are gene-encoded low-molecular-weight antibacterial peptides secreted by Enterobacteriaceae. They are involved in the regulation of microbial competitions within the intestinal microflora. Similar to bacteriocins from lactic acid bacteria, microcins exert potent bactericidal activity directed against phylogenetically-related bacterial strains, with low minimal inhibitory concentrations in the nanomolar range. However, they distinguish from bacteriocins by displaying a great structural diversity among the less than ten representatives characterized until now. Nonetheless, genetic systems encoding microcins share a conserved organization. Microcins exhibit very complex mechanisms of bactericidal activity involving several steps: (i) recognition by outer membrane receptors used for vital functions in bacteria that have been piratized by microcins; (ii) translocation of the antibacterial peptide into the periplasm; (iii) bacterial killing process that involves either interaction with the inner membrane to form a toxic structure, or passage through the inner membrane to interact with a cytoplasmic target. Microcin E492m (MccE492m) is a hydrophobic and anionic 84-amino acid peptide endowed with a C-terminal posttranslational modification, which mimics a catechol type siderophore; it targets the inner membrane of sensible bacteria in a TonB- and energy-dependent manner. Microcin J25 (MccJ25) is a 21-residue cyclic peptide with a unique lasso-type three-dimensional structure that inhibits RNA polymerase. Despite their low structural homology and different killing mechanisms, these microcins have a similar import pathway into sensible bacteria that uses siderophore receptors responsible for iron transport into bacteria. Microcin C7/C51 (MccC7/C51) is a short peptide linked to a nucleotide. It is not recognized by these receptors. In order to identify the structural regions involved in the recognition/translocation step and the killing mechanism, we studied the structure-function relationships for these three microcins.
Cancer Detection and Quantification of Treatment Response Using Diffusion-Weighted MRI (2021)

Investigation and adaptation of imaging modalities for providing additional sensitivity and expanded applications for cancer treatment response assessment is a significant area of active research. Examples span advancing image instrumentation hardware, development of new digital image acquisition capabilities, use of computer-assisted image diagnosis including artificial intelligence and deep learning, image quantification, and automation to provide robust and reproducible prognostic and diagnostic methodologies. This chapter focuses on functional advances and applications of diffusion-weighted MRI (DWI) [12,13] as it has emerged as a widely applicable approach for diagnosis, treatment planning, and assessment of response/recurrence of solid malignancies. MRI is an attractive imaging modality for tumor assessment as it provides high spatial resolution along with excellent soft-tissue contrast aiding radiographic detection and assessment of tumor. Diffusion-weighted imaging offers a unique contrast mechanism along with the ability to be used as a biomarker for the detection of changes in tumor cellular density during cancer treatment. As loss of cellular membrane integrity and overall cellularity can occur earlier than volumetric shrinkage of a tumor mass, DWI has been actively investigated as an early surrogate of cancer treatment response across solid tumor types in both animal models and human subjects. This chapter provides a succinct overview of DWI in the context of oncological research and clinical trials.