gebhart/patrepeval huggingface dataset:
Quantenpunkt‐Biosensoren für hochempfindliche Multiplexdiagnostik (2010)

Bunte Bioassays: Die zeit- und farbauflösende Detektion des resonanten Förster-Energietransfers (FRET) von lumineszierenden Terbiumkomplexen zu Halbleiter-Quantenpunkten ermöglicht Fünffach-Parallelassays mit sub-pikomolaren Nachweisgrenzen für alle fünf Bioanalyten (siehe Bild). Die Detektion der bis zu fünf Biomarker gelingt mit einer Empfindlichkeit, die 40- bis 240-mal besser ist als mit einem der besten etablierten Einzelanalyt-Referenzassays.
A Novel Brighter Bioluminescent Fusion Protein Based on ZZ Domain and Amydetes vivianii Firefly Luciferase for Immunoassays (2021)

Immunoassays are widely used for detection of antibodies against specific antigens in diagnosis, as well as in electrophoretic techniques such as Western Blotting. They usually rely on colorimetric, fluorescent or chemiluminescent methods for detection. Whereas the chemiluminescence methods are more sensitive and widely used, they usually suffer of fast luminescence decay. Here we constructed a novel bioluminescent fusion protein based on the N-terminal ZZ portion of protein A and the brighter green-blue emitting <i>Amydetes vivianii</i> firefly luciferase. In the presence of D-luciferin/ATP assay solution, the new fusion protein, displays higher bioluminescence activity, is very thermostable and produces a sustained emission (t<sub>1/2</sub> > 30 min). In dot blots, we could successfully detect rabbit IgG against firefly luciferases, Limpet Haemocyanin, and SARS-CoV-2 Nucleoprotein (1-250 ng), as well as the antigen bound antibodies using either CCD imaging, and even photography using smartphones. Using CCD imaging, we could detect up to 100 pg of SARS-CoV-2 Nucleoprotein. Using this system, we could also successfully detect firefly luciferase and SARS-CoV-2 nucleoprotein in Western Blots (5-250 ng). Comparatively, the new fusion protein displays slightly higher and more sustained luminescent signal when compared to commercial HRP-labeled secondary antibodies, constituting a novel promising alternative for Western Blotting and immunoassays.
Radiologic-Pathologic Correlation of the CT Halo Sign in Invasive Pulmonary Aspergillosis (1987)

Invasive pulmonary aspergillosis in the immunocompromised host is difficult to diagnose. Early therapy with amphotericin B improves survival. We correlated early pathologic findings with high-resolution CT of a fixed-inflated air-dried lung obtained from an autopsied patient with invasive pulmonary aspergillosis. Two distinct types of lesions were found radiologically. A large zone of air space consolidation was shown to be a confluent bronchopneumonia, and small halo-like lesions were shown to correspond to a central fungal nodule surrounded by a rim of coagulative necrosis. The halo lesion may represent an early specific sign by which invasive pulmonary aspergillosis can be diagnosed.
Engaging Aldehydes in CuH-Catalyzed Reductive Coupling Reactions: Stereoselective Allylation from 1,3-Diene Pronucleophiles (2019)

Recently, CuH-catalyzed reductive coupling processes involving carbonyl compounds and imines has become an attractive alternative to traditional methods for stereoselective addition to carbonyls due to the ability to use readily accessible and stable olefin-derived pronucleophiles as surrogates for organometallic reagents. However, the inability to use aldehydes, which traditionally reduce too rapidly in the presence of copper hydride complexes to be viable substrates, has been a major limitation. We show that by exploiting relative concentration effects through slow addition, we can invert this intrinsic reactivity and achieve the reductive coupling of 1,3-dienes with aldehydes. Using this method, both aromatic and aliphatic aldehydes can be transformed to valuable products with high levels of diastereo-and enantioselectivity and in the presence of many useful functional groups. Furthermore, using a combination of theoretical (DFT) and experimental methods, important mechanistic features of this reaction related to stereo-and chemoselectivity were uncovered. Computational details and Cartesian coordinates of optimized geometries
Essential role of ubiquitin C‐terminal hydrolases UCHL1 and UCHL3 in mammalian oocyte maturation (2011)

Ubiquitin C-terminal hydrolases (UCHs) comprise a family of deubiquitinating enzymes that play a role in the removal of multi-ubiquitin chains from proteins that are posttranslationally modified by ubiquitination to be targeted for proteolysis by the 26S proteasome. The UCH-enzymes also generate free monomeric ubiquitin from precursor multi-ubiquitin chains and, in some instances, may rescue ubiquitinated proteins from degradation. This study examined the roles of two oocyte-expressed UCHs, UCHL1, and UCHL3 in murine and rhesus monkey oocyte maturation. The Uchl1 and Uchl3 mRNAs were highly expressed in GV and MII oocytes, and were associated with the oocyte cortex (UCHL1) and meiotic spindle (UCHL3). Microinjection of the UCH-family enzyme inhibitor, ubiquitin-aldehyde (UBAL) to GV oocytes prevented oocyte meiotic progression beyond metaphase I in a majority of treated oocytes and caused spindle and first polar body anomalies. Injection of antibodies against UCHL3 disrupted oocyte maturation and caused meiotic anomalies, including abnormally long meiotic spindles. A selective, cell permeant inhibitor of UCHL3, 4, 5, 6, 7-tetrachloroidan-1, 3-dione also caused meiotic defects and chromosome misalignment. Cortical granule localization in the oocyte cortex was disrupted by UBAL injected after oocyte maturation. We conclude that the activity of oocyte UCHs contributes to oocyte maturation by regulating the oocyte cortex and meiotic spindle.
A Polymerase Chain Reaction (PCR) Method for Sex and Species Determination with Novel Controls for Deoxyribonucleic Acid (DNA) Template Length (1992)

Human X and Y chromosome alpha-satellite sequences lying within higher order repeats were amplified by the polymerase chain reaction (PCR) in genomic deoxyribonucleic acid (DNA) isolated from blood, bone, and several other tissues and specimens of potential forensic science interest. X and Y sequences could be coamplified under some of the PCR conditions employed. Monomorphic sequences in the 3'-apolipoprotein B gene (designated "H") and in an alpha-satellite higher order repeat on Chromosome 17 (p17H8, D17Z1) were likewise amplified in the specimens. X and Y sequence amplification can provide information about the sex of origin. Amplification of the X, H, and D17Z1 sequences was found to be primate-specific among the common animals tested and can thus provide species of origin information about a specimen. The authors suggest that amplification of X and D17Z1 or H sequences might provide "relaxed" and "stringent" controls for appropriate PCR amplification tests on forensic science specimens. Testing was carried out using PCR protocols that employed Thermophilus aquaticus (Taq) and Thermus flavis (Replinase) thermostable DNA polymerases.
Soil Characteristics Under Coppice Sal ( Shorea robusta ) in the Lateritic Region of West Bengal (1989)

The nature and properties of some coppice Sal ( Shorea robusta ) growing soils in the lateritic region of W. Bengal were studied in order to evaluate tbe characteristics of the soils supporting this species. Out of 31 sites, 23 sites bad GBH greater than the table values suggesting tbat these sites were very much favourable for optimum growth of Sal (coppice). Ranges of some of the soil attributes suitable for the optimum growth of the species under more or less similar climatic conditions were assessed.
Pilot randomized controlled trial of a comprehensive smoking cessation intervention for patients with upper aerodigestive cancer undergoing radiotherapy (2018)

This intervention decreased smoking among patients with upper aerodigestive cancers during radiotherapy.
Future research needs in the field of HPFRCC (2004)

Peer Reviewed
Small Peptide Analogue of SDF-1α Supports Survival of Cord Blood CD34+ Cells in Synergy with Other Cytokines and Enhances Their Ex Vivo Expansion and Engraftment into Nonobese Diabetic/Severe Combined Immunodeficient Mice (2005)

The SDF-1/CXCR4 axis has been implicated in the chemotaxis, homing, mobilization, and expansion of hematopoietic stem and progenitor cells. We studied the effects of a SDF-1 peptide analogue CTCE-0214 on the survival of cord blood CD34+ cells in culture, expansion, and engraftment of expanded cells in the nonobese diabetic/severe combined immunodeficient (NOD/SCID) mouse model. Our results demonstrated that CTCE-0214 synergized with thrombopoietin (TPO), stem cell factor (SCF), or flt-3 ligand (FL) on the survival of stem and progenitor cells in culture. Adding CTCE-0214 at a low concentration (0.01 ng/ml) for 4 days together with TPO, SCF, and FL significantly enhanced ex vivo expansion of CD34+ cells to subsets of primitive (CD34+CD38- cells, colony-forming unit-mixed [CFU-GEMMs]), erythroid (CFU-Es), myeloid (CFU-GMs), and megakaryocytic (CD61+CD41+ cells, CFU-MKs) progenitors, as well as their multilineage engraftment in NOD/SCID mice. Interestingly, the short exposure of expanded cells to CTCE-0214 (100 and 500 ng/ml) for 4 hours did not increase the quantity of progenitor cells but enhanced their engraftment capacity. The proportion of CD34+ cells expressing surface CXCR4 was decreased, but the overall number of this population increased upon expansion. The small peptide analogue of SDF-1 could be developed for ex vivo expansion and improving engraftment of cord blood transplantation.
Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology (2022)

A major limitation of gene expression biomarker studies is that they are not reproducible as they simply do not generalize to larger, real-world, heterogeneous populations. Frequentist multi-cohort gene expression meta-analysis has been frequently used as a solution to this problem to identify biomarkers that are truly differentially expressed. However, the frequentist meta-analysis framework has its limitations-it needs at least 4-5 datasets with hundreds of samples, is prone to confounding from outliers and relies on multiple-hypothesis corrected p-values. To address these shortcomings, we have created a Bayesian meta-analysis framework for the analysis of gene expression data. Using real-world data from three different diseases, we show that the Bayesian method is more robust to outliers, creates more informative estimates of between-study heterogeneity, reduces the number of false positive and false negative biomarkers and selects more generalizable biomarkers with less data. We have compared the Bayesian framework to a previously published frequentist framework and have developed a publicly available R package for use.
Tumor Necrosis Factor-α Drives 70% of Cigarette Smoke–induced Emphysema in the Mouse (2004)

Mice lacking tumor necrosis factor-alpha (TNF-alpha) receptors (TNFRKO mice) do not develop an inflammatory infiltrate or matrix breakdown after a single acute cigarette smoke exposure. To determine the role of TNF-alpha in the long-term development of emphysema, mice were exposed to smoke for 6 months. TNFRKO mice demonstrated an 11% increase in mean linear intercept; wild-type mice had a 38% increase. TNFRKO mice had 65% fewer neutrophils and no increase in macrophages in lavage fluid. Whole lung matrix metalloprotease (MMP)-2, MMP-9, MMP-12, MMP-13, and matrix type-1 (MT1)-MMP proteins were increased in wild-type mice, but smaller increases in MMP-12, MMP-13, and MT1-MMP were also seen in TNFRKO mice. Lavage matrix breakdown products were elevated in wild-type mice and only partially reduced by anti-neutrophil antibody, implying both neutrophil- and non-neutrophil-mediated matrix breakdown. We conclude that TNF-alpha-mediated processes, probably driving neutrophil influx, are responsible for approximately 70% of airspace enlargement and the majority of inflammatory cell influx/matrix breakdown in the mouse model. TNF-alpha causes increased MMP production, but some increased MMP activity is present even in TNFRKO mice. These findings imply a second TNF-alpha-independent process, possibly related to direct MMP attack on matrix, that produces the remaining 30% of airspace enlargement.
Template-Directed Self-Assembly of 10-μm-Sized Hexagonal Plates (2002)

This article presents a strategy for the fabrication of ordered microstructures using concepts of design inspired by molecular self-assembly and template-directed synthesis. The self-assembling components are 4-μm-thick hexagonal metal plates having sides 10 μm in length (“hexagons”), and each template consists of a 4-μm-thick circular metal plate surrounding a central cavity, the perimeter of which is complementary in shape to the external edges of a two-dimensional, close-packed array of hexagons. The hexagons and templates (collectively, “pieces”) were fabricated via standard procedures and patterned into hydrophobic and hydrophilic regions using self-assembled monolayers (SAMs). Templated self-assembly occurs in water through capillary interactions between thin films of a nonpolar liquid adhesive coating the hydrophobic faces of the pieces. The hexagons tile the cavities enclosed by the templates, and the boundaries of the cavities determine the sizes and shapes of the assemblies. Curing the adhesive with ultraviolet light furnishes mechanically stable arrays having well-defined morphologies. By allowing control over the structures of the resulting aggregates, this work represents a step toward the development of practical methods for microfabrication based on self-assembly.
Scalable Mismatch Compensation for Time-Interleaved A/D Converters in OFDM Reception (2010)

Realization of all-digital baseband receiver processing for multi-Gigabit communication requires analog-to-digital converters (ADCs) of sufficient rate and output resolution. A promising architecture for this purpose is the time-interleaved ADC (TI-ADC), in which several "sub-ADCs" are employed in parallel. However, the timing mismatch between the sub-ADCs, if left uncompensated, leads to error floors in receiver performance. Standard linear digital mismatch compensation (e.g., based on the zero-forcing criterion) requires a number of taps that increases with the desired resolution. In this paper, we show that oversampling provides a scalable (in the number of sub-ADCs and in the desired resolution) approach to mismatch compensation, allowing elimination of mismatch-induced error floors at reasonable complexity. While the structure of the interference due to mismatch is different from that due to a dispersive channel, there is a strong analogy between the role of oversampling for mismatch compensation and for channel equalization. We illustrate the efficacy of the proposed mismatch compensation techniques for an OFDM receiver.
Novel Potent Capsid Assembly Modulators Regulate Multiple Steps of the Hepatitis B Virus Life Cycle (2018)

The assembly of hepatitis B virus (HBV) core protein (HBc) into capsids represents a critical step of viral replication. HBc has multiple functions during the HBV life cycle, which makes it an attractive target for antiviral therapies. Capsid assembly modulators (CAMs) induce the formation of empty capsid or aberrant capsid devoid of pregenomic RNA (pgRNA) and finally block relaxed circular DNA neosynthesis and virion progeny. In this study, the novel CAMs JNJ-827 and JNJ-890 were found to be potent inhibitors of HBV replication with respective half-maximal effective concentrations of 4.7 and 66 nM, respectively, in HepG2.117 cells. Antiviral profiling in differentiated HepaRG (dHepaRG) cells and primary human hepatocytes revealed that these compounds efficiently inhibited HBV replication, as well as <i>de novo</i> establishment of covalently closed circular DNA (cccDNA). In addition to these two known effects of CAMs, we observed for the first time that a CAM, here JNJ-827, when added postinfection for a short-term period, significantly reduced hepatitis B e antigen (HBeAg) secretion without affecting the levels of cccDNA amount, transcription, and hepatitis B surface antigen (HBsAg) secretion. This inhibitory activity resulted from a direct effect of JNJ-827 on HBeAg biogenesis. In a long-term treatment condition using persistently infected dHepaRG cells, JNJ-827 and JNJ-890 reduced HBsAg concomitantly with a decrease in viral total RNA and pgRNA levels. Altogether, these data demonstrate that some CAMs could interfere with multiple functions of HBc in the viral life cycle.
Volumetric retinal imaging with ultrahigh-resolution spectral-domain optical coherence tomography and adaptive optics using two broadband light sources (2009)

Ultrabroadband sources, such as multiplexed superluminescent diodes (SLDs) and femtosecond lasers, have been successfully employed in adaptive optics optical coherence tomography (AO-OCT) systems for ultrahigh resolution retinal imaging. The large cost differential of these sources, however, motivates the need for a performance comparison. Here, we compare the performance of a Femtolasers Integral Ti:Sapphire laser and a Superlum BroadLighter T840, using the same AO-OCT system and the same subject. In addition, we investigate the capability of our instrument equipped with the Integral to capture volume images of the fovea and adjacent regions on a second subject using the AO to control focus in the retina and custom and freeware image registration software to reduce eye motion artifacts. Monochromatic ocular aberrations were corrected with a woofer-tweeter AO system. Coherence lengths of the Integral and BroadLighter were measured in vivo at 3.2 microm and 3.3 microm, respectively. The difference in dynamic range was 5 dB, close to the expected variability of the experiment. Individual cone photoreceptors, retinal capillaries and nerve fiber bundles were distinguished in all three dimensions with both sources. The acquired retinal volumes are provided for viewing in OSA ISP, allowing the reader to data mine at the microscope level.
Proteome-wide Analysis in Saccharomyces cerevisiae Identifies Several PHD Fingers as Novel Direct and Selective Binding Modules of Histone H3 Methylated at Either Lysine 4 or Lysine 36 (2006)

The PHD finger motif is a signature chromatin-associated motif that is found throughout eukaryotic proteomes. Here we have determined the histone methyl-lysine binding activity of the PHD fingers present within the Saccharomyces cerevisiae proteome. We provide evidence on the genomic scale that PHD fingers constitute a general class of effector modules for histone H3 trimethylated at lysine 4 (H3K4me3) and histone H3 trimethylated at lysine 36 (H3K36me3). Structural modeling of PHD fingers demonstrates a conserved mechanism for recognizing the trimethyl moiety and provides insight into the molecular basis of affinity for the different methyl-histone ligands. Together, our study suggests that a common function for PHD fingers is to transduce methyl-lysine events and sheds light on how a single histone modification can be linked to multiple biological outcomes.
Clinical management of sickle cell liver disease in children and young adults (2020)

Liver involvement in sickle cell disease (SCD) is often referred to as sickle cell hepatopathy (SCH) and is a complication of SCD which may be associated with significant mortality. This review is based on a round-table workshop between paediatric and adult hepatologists and haematologists and review of the literature. The discussion was prompted by the lack of substantial data and guidance in managing these sometimes very challenging cases. This review provides a structured approach for the diagnosis and management of SCH in children and young adults. The term SCH describes any hepatobiliary dysfunction in the context of SCD. Diagnosis and management of biliary complications, acute hepatic crisis, acute hepatic sequestration and other manifestations of SCH are discussed, as well as the role of liver transplantation and haemopoietic stem cell transplantation in the management of SCH.
ChemInform Abstract: Generality of the Reaction of Diazomethane with Halogenoplatinum(II) Complexes in the Preparation of (Halogenomethyl)platinum(II) Complexes. (1988)

Abstract Treatment of a range of Pt(II) halide (mainly chloride) complexes with diazomethane is examined.
Chemically Coupled Conducting Complex Framework Materials (C4FMs) As Sulfur Hosts in Lithium – Sulfur Batteries (2017)

Abstract Ever increasing demand for efficient portable energy storage systems has directed researchers towards finding alternatives for the conventional insertion – based lithium-ion battery cathodes. Sulfur, with a theoretical specific capacity of 1672 mAh/g is a promising candidate for high energy density lithium battery cathodes1, 2. Low cost and ease of availability further adds to the advantages of sulfur over hitherto transition metal – based cathodes. However, elemental sulfur has very low electronic conductivity (~10-15 S/cm)3 at room temperature which restricts the active material utilization in Li – S battery. The formation of soluble non – intercalation based polysulfide intermediates (Li2Sn; n = 2 – 8)4 during electrochemical cycling further results in active material loss by coating onto the anode leading to eventual battery failure. Embedding sulfur into porous materials have shown considerable reduction in polysulfide dissolution by preventing direct contact with the liquid electrolyte5-7. However, inability to precisely control porosity and lack of chemical interaction between these porous structures and the entrapped sulfur greatly limits the efficiency of this approach. To completely prevent polysulfide dissolution, sulfur hosts with tunable, engineered porosity and increased affinity for polysulfide needs to be engineered. In this work, chemically coupled conductive complex framework materials (C4FMs) with nanoporous structure were used as hosts for sulfur in Li – S battery. Introduction of special functional groups improves the affinity of these structures towards polysulfide. The frameworks were synthesized using microwave assisted hydrothermal synthesis and then infiltrated with sulfur using vapor infiltration techniques. These sulfur – hosted cathodes showed a stable electrochemical performance with an initial discharge capacity of ~1620 mAh/g which stabilized at 1100 mAh/g to100 cycles (Figure 1). Acknowledgements: The authors acknowledge the financial support of DOE grant DE-EE 0006825, Edward R. Weidlein Chair Professorship funds and the Center for Complex Engineered Multifunctional Materials (CCEMM). References 1. J. R. Akridge, Y. V. Mikhaylik and N. White, Solid State Ionics, 2004, 175, 243-245. 2. M. M. Thackeray, C. Wolverton and E. D. Isaacs, Energy &amp; Environmental Science, 2012, 5, 7854-7863. 3. M. Edeling, R. W. Schmutzler and F. Hensel, Philosophical Magazine Part B, 1979, 39, 547-550. 4. S. S. Zhang, Journal of Power Sources, 2013, 231, 153-162. 5. S.-R. Chen, Y.-P. Zhai, G.-L. Xu, Y.-X. Jiang, D.-Y. Zhao, J.-T. Li, L. Huang and S.-G. Sun, Electrochimica Acta, 2011, 56, 9549-9555. 6. Z. Gong, Q. Wu, F. Wang, X. Li, X. Fan, H. Yang and Z. Luo, RSC Advances, 2016, 6, 37443-37451. 7. J. Jin, Z. Wen, G. Ma, Y. Lu and K. Rui, Solid State Ionics, 2014, 262, 170-173. Figure 1