gebhart/patrepeval huggingface dataset:
Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures—Gender matters (2019)

Urothelial cancer (UCa) is the most predominant cancer of the urinary tract and noninvasive diagnosis using hypermethylation signatures in urinary cells is promising. Here, we assess gender differences in a newly identified set of methylation biomarkers. UCa-associated hypermethylated sites were identified in urine of a male screening cohort (n = 24) applying Infinium-450K-methylation arrays and verified in two separate mixed-gender study groups (n = 617 in total) using mass spectrometry as an independent technique. Additionally, tissue samples (n = 56) of mixed-gender UCa and urological controls (UCt) were analyzed. The hypermethylation signature of UCa in urine was specific and sensitive across all stages and grades of UCa and independent on hematuria. Individual CpG sensitivities reached up to 81.3% at 95% specificity. Albeit similar methylation differences in tissue of both genders, differences were less pronounced in urine from women, most likely due to the frequent presence of squamous epithelial cells and leukocytes. Increased repression of methylation levels was observed at leukocyte counts ≥500/μl urine which was apparent in 30% of female and 7% of male UCa cases, further confirming the significance of the relative amounts of cancerous and noncancerous cells in urine. Our study shows that gender difference is a most relevant issue when evaluating the performance of urinary biomarkers in cancer diagnostics. In case of UCa, the clinical benefits of methylation signatures to male patients may outweigh those in females due to the general composition of women's urine. Accordingly, these markers offer a diagnostic option specifically in males to decrease the number of invasive cystoscopies.
Applications of Enzymatically Prepared Homochiral Cyclohexane Building Blocks: Enantioselective Synthesis of Derivatives of Unnatural Shikimic Acid and of Pseudo-α-D-mannopyranose (1992)

The utility of (1R,2S,3R,4S)-4-butanoyloxy-2,3-O-isopropylidenecyclohexane-1,2,3-triol [(+)-1] as a homochiral building block is illustrated by its transformation into the unnatural enantiomer of methyl shikimate [(+)-10] and into pseudo-α-D-mannopyranose [(+)-14].
Diagnostic accuracy of faecal immunochemical test for screening individuals with a family history of colorectal cancer (2013)

Compared with colonoscopy, FIT is more likely to miss advanced neoplasms or cancers in individuals with a family history of CRC.
TheBacillus subtilisscRNA is related to the 4.5S RNA fromEscherichia coli (1988)

Journal Article The Bacillus subtilis scRNA is related to the 4.5S RNA from Escherichia coli Get access Joachim C.R. Struck, Joachim C.R. Struck Freie Universität Berlin, Institut für BiochemieThielallee 63, D-1000 Berlin 33, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Detlef W. Vogel, Detlef W. Vogel Freie Universität Berlin, Institut für BiochemieThielallee 63, D-1000 Berlin 33, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nobert Ulbrich, Nobert Ulbrich Freie Universität Berlin, Institut für BiochemieThielallee 63, D-1000 Berlin 33, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Volker A. Erdmann Volker A. Erdmann Freie Universität Berlin, Institut für BiochemieThielallee 63, D-1000 Berlin 33, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 6, 25 March 1988, Page 2719, https://doi.org/10.1093/nar/16.6.2719 Published: 25 March 1988 Article history Received: 22 February 1988 Published: 25 March 1988
Self‐Assembled Surface Patterns of Binary Colloidal Crystals (2003)

Co‐assembly of binary dispersions of monodisperse microspheres with large size ratios has been used to produce well‐ordered hexagonally close‐packed monolayers of large spheres with a superimposed pattern of small spheres (see Figure). The architectures obtained are determined by the size and concentration ratios of the microspheres in the dispersions, are very diverse, and can be obtained reproducibly over millimeter length scales.
Novel patterning schemes and technologies for the sub 5nm era (2018)

Multipatterning has enabled continued scaling of chip technology at the 28nm logic node and beyond see Fig. 1. Self-aligned double patterning (SADP) and self-aligned quadruple patterning (SAQP) as well as Litho-Etch/Litho-Etch iterations are widely used in the semiconductor industry to reach sub 193 immersion lithography resolutions for critical layers such as FIN, Gate and Metal lines. Multipatterning requires the use of multiple masks, which is costly and increases process complexity as well as edge placement error variation mostly driven by overlay. In our presentation, we will propose and demonstrate novel patterning concepts, which can curb some of these downsides and usher in the next technological advancements required for further scaling. We will also survey the progress and maturity of EUV patterning in contrast to multipatterning options.
In search of a good fit: CPAP therapy mask selection for obstructive sleep apnoea (2018)

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Differential proteomic analysis for the evaluation of protein expression in fresh human cortical brain biopsies (2016)

Mammalian brain is challenging to study due to its heterogeneity and complexity. However, recent advances in molecular imaging, genomics and proteomics have contributed significantly to achieve insights into molecular basis of brain function and pathogenesis of neurological disorders. Efficient sample preparation is an integral part of a successful mass spectrometry (MS)-based proteomics. Apart from the identification, quantification of proteins is needed to investigate the alterations between proteome profiles from different sample sets. Therefore, this thesis investigates optimizing and application of the MS compatible sample preparation techniques for the identification and quantification of proteins from brain tissue.The central objective of this thesis was (i) to improve the extraction of proteins as well as membrane proteins (MPs) from the brain tissue and (ii) to apply the optimized method along with the stable isotope dimethyl labeling (DML) and label-free (LF) MS approaches for the relative quantification of the brain proteome profiles during neurological conditions such as Alzheimer’s disease (AD) and traumatic brain injury (TBI). First study described in this thesis is focused on the qualitative aspects for the brain tissue sample preparation. The optimized extraction buffers from first study containing n-octyl-β-glucopyranside or triton X-114 were used in the further quantitative studies to extract the proteins from patient (AD or TBI) and control human brain samples. Triton X-114 has additional advantage of separating MPs into a micellar phase. Therefore we also investigated the possibility to apply this in combination with DML quantitation approach for enrichment of low abundant MPs from AD brains.AD and TBI causes severe socio-economic burden on the society and therefore there is a need to develop diagnostic markers to detect the early changes in the pathology of the disease. Analytical tools and techniques applied and discussed in this thesis for neuroproteomics applications proved to be powerful and reliable for analyzing complex biological samples to generate high-throughput screening and unbiased identification and quantitation of disease-specific proteins that are of great importance in understanding the disease pathology.
Deducing the Adsorption Geometry of Rhodamine 6G from the Surface-Induced Mode Renormalization in Surface-Enhanced Raman Spectroscopy (2017)

Surface-enhanced Raman spectroscopy probes adsorbates on a plasmonic substrate and offers high sensitivity with molecular identification capabilities. In this study, we present a refined methodology for considering the supporting substrate in the computation of the Raman spectra. The supporting substrate is taken into account by employing a periodic slab model when doing the geometry optimization and normal mode analysis, and then the Raman spectrum is calculated for the isolated molecule but with the normal modes from the surface structure. We find that the interaction with the surface induces internal distortion in the molecule, and spectral shifts in the computed Raman spectrum. By comparing a low temperature surface-enhanced Raman spectroscopy measurement of Rhodamine 6G (R6G) with the computed Raman spectra of a series of adsorption geometries, we propose that the binding state captured in the experiment tends to possess the least internal distortion. This binding state involves upward orientation of ethylamine on R6G, and our calculations indicate that this is the lowest energy adsorption structure. Following this route, it is possible to infer both a molecular orientation and an adsorption geometry of the molecule from its Raman spectrum. Importantly, we note that, if the substrate correction is established to play a role, we also discuss that this corrected approach still has several shortcomings that significantly limit its overall accuracy in comparison with experimental spectra.
IQ: The Case for Iterative Querying for Knowledge (2011)

Large knowledge bases, the Linked Data cloud, and Web 2.0 communities open up new opportunities for deep question answering to support the advanced information needs of knowledge workers like students, journalists, or business analysts. This calls for going beyond keyword search, towards more expressive ways of entity-relationship-oriented querying with graph constraints or even full-fledged languages like SPARQL (over graph-structured, schema-less data). However, a neglected aspect of this active research direction is the need to support also query refinements, relaxations, and interactive exploration, as single-shot queries are often insufficient for the users ’ tasks. This paper addresses this issue by discussing the paradigm of Iterative Querying, IQ for short. We present two instantiations for IQ, one based on keyword search over labeled graphs combined with structural constraints, and another one based on extensions of the SPARQL language. We discuss the suitability of these approaches for knowledge-centric search tasks, and we identify open research problems that deserve greater attention. 1.
Measuring Neural Entrainment to Beat and Meter in Infants: Effects of Music Background (2016)

Caregivers often engage in musical interactions with their infants. For example, parents across cultures sing lullabies and playsongs to their infants from birth. Behavioral studies indicate that infants not only extract beat information, but also group these beats into metrical hierarchies by as early as 6 months of age. However, it is not known how this is accomplished in the infant brain. An EEG frequency-tagging approach has been used successfully with adults to measure neural entrainment to auditory rhythms. The current study is the first to use this technique with infants in order to investigate how infants' brains encode rhythms. Furthermore, we examine how infant and parent music background is associated with individual differences in rhythm encoding. In Experiment 1, EEG was recorded while 7-month-old infants listened to an ambiguous rhythmic pattern that could be perceived to be in two different meters. In Experiment 2, EEG was recorded while 15-month-old infants listened to a rhythmic pattern with an unambiguous meter. In both age groups, information about music background (parent music training, infant music classes, hours of music listening) was collected. Both age groups showed clear EEG responses frequency-locked to the rhythms, at frequencies corresponding to both beat and meter. For the younger infants (Experiment 1), the amplitudes at duple meter frequencies were selectively enhanced for infants enrolled in music classes compared to those who had not engaged in such classes. For the older infants (Experiment 2), amplitudes at beat and meter frequencies were larger for infants with musically-trained compared to musically-untrained parents. These results suggest that the frequency-tagging method is sensitive to individual differences in beat and meter processing in infancy and could be used to track developmental changes.
Tissue engineering and regenerative medicine (2016)

Clinical applications of skin substitutes primarily include burn injuries and chronic wounds. Tissue-engineered vessels appear to be the next generation of small-diameter bypass grafts, addressing the growing need for alternative materials for small-caliber arterial replacement. There have been many different large-animal studies, many of which have produced encouraging results that have made it possible to investigate putative bone tissue engineering strategies. Synthetic polymers such as PLA and PGA were initially investigated as cartilage scaffolds early in the study of cartilage tissue engineering. In addition to replacing damaged cardiac tissue, cardiac tissue engineering can be used to reconstruct pediatric congenital defects. The objective of urinary tissue engineering is to provide an alternative source of tissue that is more similar to native bladder or urethra. Continued progress toward reliable and reproducible graft success can position corneal tissue engineering as an important alternative to conventional donor based techniques.
Phase I Trial on sms‐D70 Somatostatin Analogue in Advanced Prostate and Renal Cell Cancer (2004)

Plasma concentrations and tolerability of a novel somatostatin analogue sms-D70 were studied in patients with metastatic hormone-resistant prostate cancer (HRPC) or metastatic renal cell cancer. To overcome the limitations of the octapeptides having affinity only to somatostatin receptor subtypes 2 and 5, HRPC expressing mainly somatostatin receptors 1 and 4, a somatostatin derivative based on the natural somatostatin having affinity to all five somatostatin receptor subtypes, was developed. The in vivo stability of this dextran-conjugated derivative, somatostatin-D70, was confirmed previously in animal studies, and the nanomolar "panaffinity" has been shown in in vitro receptor binding studies on cell lines transfected with the somatostatin receptor genes. Sms-D70 was given with subcutaneous injection once a week at dose levels of 5, 10, 20, 35, and 50 mg. For pharmacokinetic studies, sms-D70 was labeled with 131I. Fourteen patients were treated, of whom 10 had prostate and 4 renal cell cancer. The kinetic data revealed high stability with a long half-life in the blood. The drug was well tolerated, and no grade 4 (WHO) toxicity was observed. The maximal tolerated dose could not be established due to the lack of dose-limiting toxicities. Objective PSA responses were not recorded in these heavily treated patients, but subjective stabilization of pain was observed and urinary symptoms were alleviated in four patients. Three patients with metastatic HRPC received 5-10-mg intravenous injections of sms-D70 once weekly for 4-14 months on a compassionate use basis. In all cases, serum PSA values decreased more than 50% from the pretreatment level, but these results are difficult to interpret due to concomitant treatments given to these patients. In conclusion, sms-D70 was well tolerated in the treatment of metastatic prostate and renal cell cancer, but no responses were found in these heavily treated patients.
Detection and Confirmation of Quantitative Trait Loci for Soybean Seed Isoflavones (2014)

ABSTRACT Interest in soybean [ Glycine max (L.) Merr.] isoflavones has increased in recent years owing to numerous reported health benefits. Consequently, quantitative trait loci (QTL) detection for marker‐assisted breeding for isoflavones is being examined for genetic gains. This study sought to detect QTL for soybean isoflavones in a population of 274 recombinant inbred lines derived from a cross between ‘Essex’ and ‘Williams 82’ that were subdivided and tested by maturity (early, mid, and late). The field tests were conducted in three environments in 2009 (Knoxville, TN; Harrisburg, IL; and Stuttgart, AR). The population was genotyped with 480 polymorphic single nucleotide polymorphism markers. Isoflavones for each replicate were analyzed by near infrared reflectance spectroscopy, whose prediction equation was based on high performance liquid chromatography. Each maturity test, containing 91 or 92 recombinant inbred lines, was analyzed separately for QTL. In total, 21 QTL were detected: 7 for genistein (chromosomes 5, 6, 9, 13, 17, and 19), 5 for daidzein (chromosomes 5, 6, 9, 13, and 19), 3 for glycitein (chromosomes 6, 9, and 20), and 6 for total isoflavone content (chromosomes 5, 6, 9, 13, and 19). Of these 21 QTL, 12 were confirmed or positional confirmations from other studies. Utilization of these QTL could potentially lead to marker‐assisted selection approaches for genetic gains in improving soybean isoflavones.
Compact optical system for pulse-to-pulse laser beam quality measurement and applications in laser machining (2004)

Fluctuations in beam quality (M2) have been observed on a pulse-to-pulse basis from an industrial Nd:YAG laser. This was achieved with a compact multiplane imaging method incorporating quadratically distorted diffraction gratings, which enabled simultaneous imaging of nine planes on a single CCD array. With this system, we measured across a range of beam qualities with an associated error (in M2 variation) of the order of 0.7%. Application of the system to fiber-optic beam delivery and laser drilling is demonstrated.
Foreign Body Granuloma Following Orbital Reconstruction with Porous Polyethylene (2014)

Porous polyethylene is commonly used in the orbit for fracture repair and anophthalmic reconstruction; it reportedly has a good safety profile and integrates well into host tissue. Foreign body reaction to porous polyethylene has been reported in facial tissue, but to our knowledge, not in the orbit. The authors report 2 cases of foreign body inflammatory giant cell reaction in patients who underwent orbital fracture repairs with porous polyethylene implants.
STEEL FIBER OR CONVENTIONAL REINFORCEMENT FOR CONCRETE SHEARWALLS (1996)

In moderately tall multistory buildings, coupled shearwalls (CSW) are a form of construction often used as a means of resisting horizontal forces due to wind and earthquake. This is due, in particular, to high in-plane stiffness of CSWs. This stiffness helps to minimize excessive lateral movement thereby providing efficient protection against nonstructural damage. Structural protection against wind and earthquake loads can be very costly in modern buildings. Numerous studies have been devoted to the understanding of the (hysteretic) complex behavior of CSWs, both theoretically and experimentally. These studies have demonstrated that it is possible to build ductile CSWs provided appropriate practical measures are taken. A research project was carried out to examine the performance of SFRC (steel fiber reinforced concrete) wall/coupling beam joint under cyclic loadings, and the results are presented here.
A Phase I Study of XL019, a Selective JAK2 Inhibitor, in Patients with Polycythemia Vera (2008)

Abstract More than 98% of patients with polycythemia vera (PV) carry the activating JAK2 mutation V617F, which may play a role in the pathogenesis of PV by promoting hematopoetic cell proliferation and survival. PV is characterized by an increased red blood cell mass and is generally accompanied by increased myeloid and megakaryocytic production. Current therapy consists of supportive care measures including aspirin, phlebotomy, interferon and hydroxyurea to reduce the risk of complications of the disease such as thrombotic events. Such palliative therapy is often unsatisfactory due to side effects and the persistent susceptibility of the patients to development of thrombosis, and the failure to prevent transformation to myelofibrosis or acute leukemia. XL019 potently and selectively inhibits JAK2 (Ki of 2 nM); relative to other JAK family kinases (JAK1 Ki of 134 nM, JAK3 Ki of 195 nM and TYK2 Ki of 344 nM). Cellular selectivity of XL019 was confirmed in primary human cell assays; while EPO-stimulated pSTAT5 in primary erythroid cells was quite sensitive to XL019 treatment (IC50 of 64 nM), stimulation of T-cells with IL-2 or B-cells with IL-4 or IL-6 gave pSTAT IC50s of &amp;gt;800 nM in each case. Potent effects on JAK2-STAT signaling were also demonstrated in single-dose pharmacodynamic studies in xenograft tumors, including HEL92.1.7, CFPAC-1 and DU 145. XL019 is being evaluated in a Phase 1 dose escalation study in subjects with PV who have failed or are intolerant of standard therapies defined as follows: symptomatic splenomegaly in spite of current therapy, thrombocytosis with a platelet count &amp;gt;450K/μl, or non-controlled constitutional symptoms such as pruritus, night sweats, or weight loss. The primary objectives of this study are to determine the safety and tolerability of XL019 when administered orally either once daily, or every Monday, Wednesday, and Friday in 28-day cycles (starting doses 10 mg QD and 25 mg QMWF). Secondary objectives include determination of the pharmacokinetics and pharmacodynamics of XL019, and to evaluate clinical response using the following endpoints: hematologic response; time to hematologic response; duration of hematologic response; phlebotomy independence; change in spleen and/or liver size; change in bone marrow morphology; impact on quality of life (QOL); and impact on functional exercise capacity. Pharmacodynamic assessments for this study include JAK2 V617F allele burden, erythropoietin-independent colony formation, changes in cytokine levels and JAK2 signaling pathways in peripheral blood mononuclear cells, and changes in bone marrow histology. Our initial findings regarding the tolerability, pharmacokinetics, pharmacodynamics, and preliminary clinical activity of XL019 in PV patients will be presented.
Supplemental Figure 1 from miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis (2023)

&lt;p&gt;Analysis of miR-196b, miR-34c-5p, miR-497/195 hypermethylation in lung cancer cell lines, PBMC, and NBEC.&lt;/p&gt;
Intravenously Administered Alphavirus Vector VA7 Eradicates Orthotopic Human Glioma Xenografts in Nude Mice (2010)

VA7 vector is apathogenic and can enter and destroy brain tumors in nude mice when administered systemically. This study warrants further elucidation of the mechanism of tumor destruction and attenuation of the VA7 virus.
The phenotypic landscape of essential human genes (2021)

Understanding the basis for cellular growth, proliferation, and function requires determining the contributions of essential genes to diverse cellular processes. Here, we combined pooled CRISPR/Cas9-based functional screening of 5,072 fitness-conferring genes in human cells with microscopy-based visualization of DNA, DNA damage, actin, and microtubules. Analysis of &gt;31 million individual cells revealed measurable phenotypes for &gt;90% of genes. Using multi-dimensional clustering based on hundreds of quantitative phenotypic parameters, we identified co-functional genes across diverse cellular activities, revealing novel gene functions and associations. Pooled live-cell screening of ∼450,000 cell division events for 239 genes further identified functional contributions to chromosome segregation. Our work creates a resource for the phenotypic analysis of core cellular processes and defines the functional landscape of essential human genes.
Imaging Primary Mouse Sarcomas After Radiation Therapy Using Cathepsin-Activatable Fluorescent Imaging Agents (2013)

In this primary murine model of STS, RT did not affect the ability of cathepsin-activated probes to differentiate between tumor and normal muscle. Cathepsin-activated probes labeled tumor cells and tumor-associated macrophages. Our results suggest that it would be feasible to include patients who have received preoperative RT in clinical studies evaluating cathepsin-activated imaging probes.