gebhart/patrepeval huggingface dataset:
Potential and pitfalls of whole transcriptome-based immunogenetic marker identification in acute lymphoblastic leukemia; a EuroMRD and EuroClonality-NGS Working Group study (2021)

Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation is crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. In a diagnostic setting, IG/TR gene rearrangements are generally identified using DNA-based PCR analysis, followed by classical Sanger sequencing or next generation sequencing (NGS) Nowadays, whole transcriptome RNA sequencing (RNAseq) is frequently used to identify fusion genes and to assign patients into distinct molecular subgroups according to WHO 2016 classification, or for protocol-based clinical decisions Hence, it would be beneficial if RNAseq data could also be used for the identification of IG/TR gene rearrangements pertaining to the leukemic clone.
Observation of Autler-Townes effect in a dispersively dressed Jaynes-Cummings system (2013)

Photon number splitting is observed in a transmon coupled to a superconducting quasi-lumped-element resonator in the strong dispersive limit. A thermal population of 5.474 GHz photons at an effective resonator temperature of T = 120mK results in a weak n = 1 photon peak along with the n = 0 photon peak in the qubit spectrum in the absence of a coherent drive on the resonator. Two-tone spectroscopy using independent coupler and probe tones reveals an Autler-Townes splitting in the thermal n = 1 photon peak. The observed effect is explained accurately using the four lowest levels of the dispersively dressed qubit-resonator system and compared to results from numerical simulations of the steady-state master equation for the coupled system.
Two‐stage dilute acid‐catalyzed hydrolytic conversion of softwood sawdust into sugars fermentable by ethanologenic microorganisms (2005)

Abstract Softwood hemlock residues generated in a sawmill were tested as a feasible agricultural feedstock for the production of high‐value bio‐based products using the concept of two‐stage dilute acid hydrolysis. To convert the carbohydrate contained in the hemlock sawdust, two‐stage dilute‐acid catalyzed hydrolysis was conducted. In the first stage, sawdust was hydrolyzed at 190 °C for 150 s with 1.1wt% sulfuric acid and 46.0 wt% total solids. As a result, 69.3% mannose, 74.2% galactose, 67.7% xylose, and 17.4% glucose of their theoretical maximum yields were achieved, which reveals that hemicellulose was the major target in the first‐stage hydrolysis. After recovering soluble sugars by washing from the first‐stage hydrolysate with water, the washed first‐stage hydrolysate solids were hydrolyzed again in the second stage at more severe conditions, such as 2.6 or 3.5 wt% H 2 SO 4 , 205 or 210 °C, and 80–135 s. After the two stages, the highest overall yields from 100 g of dry hemlock sawdust were a total of 39.3 g of fermentable sugars (36.0 and 3.3 g of hexose and pentose sugars, respectively). These results indicate that hemlock sawdust could be used to produce fermentable sugars which can be converted into other value‐added bio‐based products. Copyright © 2005 Society of Chemical Industry
Pediatric acute myeloid leukemia with t(8;16)(p11;p13), a distinct clinical and biological entity: a collaborative study by the International-Berlin-Frankfurt-Münster AML-study group (2013)

In pediatric acute myeloid leukemia (AML), cytogenetic abnormalities are strong indicators of prognosis. Some recurrent cytogenetic abnormalities, such as t(8;16)(p11;p13), are so rare that collaborative studies are required to define their prognostic impact. We collected the clinical characteristics, morphology, and immunophenotypes of 62 pediatric AML patients with t(8;16)(p11;p13) from 18 countries participating in the International Berlin-Frankfurt-Münster (I-BFM) AML study group. We used the AML-BFM cohort diagnosed from 1995-2005 (n = 543) as a reference cohort. Median age of the pediatric t(8;16)(p11;p13) AML patients was significantly lower (1.2 years). The majority (97%) had M4-M5 French-American-British type, significantly different from the reference cohort. Erythrophagocytosis (70%), leukemia cutis (58%), and disseminated intravascular coagulation (39%) occurred frequently. Strikingly, spontaneous remissions occurred in 7 neonates with t(8;16)(p11;p13), of whom 3 remain in continuous remission. The 5-year overall survival of patients diagnosed after 1993 was 59%, similar to the reference cohort (P = .14). Gene expression profiles of t(8;16)(p11;p13) pediatric AML cases clustered close to, but distinct from, MLL-rearranged AML. Highly expressed genes included HOXA11, HOXA10, RET, PERP, and GGA2. In conclusion, pediatric t(8;16)(p11;p13) AML is a rare entity defined by a unique gene expression signature and distinct clinical features in whom spontaneous remissions occur in a subset of neonatal cases.
Replication of porcine circoviruses (2009)

Porcine circoviruses are circular single-stranded DNA viruses that infect swine and wild boars. Two species of porcine circoviruses exist. Porcine circovirus type 1 is non pathogenic contrary to porcine circovirus type 2 which is associated with the disease known as Post-weaning Multisystemic Wasting Syndrome. Porcine circovirus DNA has been shown to replicate by a rolling circle mechanism. Other studies have revealed similar mechanisms of rolling-circle replication in plasmids and single-stranded viruses such as Geminivirus. Three elements are important in rolling-circle replication: i) a gene encoding initiator protein, ii) a double strand origin, and iii) a single strand origin. However, differences exist between viruses and plasmids and between viruses. Porcine circovirus replication probably involves a "melting pot" rather than "cruciform" rolling-circle mechanism.This review provides a summary of current knowledge of replication in porcine circoviruses as models of the Circovirus genus. Based on various studies, the factors affecting replication are defined and the mechanisms involved in the different phases of replication are described or proposed.
Novel post-translational modifications of Smad2 identified by mass spectrometry (2008)

Abstract Smad2 is a crucial component of transforming growth factor-β (TGFβ) signaling, and is involved in the regulation of cell proliferation, death and differentiation. Phosphorylation, ubiquitylation and acetylation of Smad2 have been found to regulate its activity. We used mass spectrometry to search for novel post-translational modifications (PTMs) of Smad2. Peptide mass fingerprinting (PMF) indicated that Smad2 can be acetylated, methylated, citrullinated, phosphorylated and palmitoylated. Sequencing of selected peptides validated methylation at Gly122 and hydroxylation at Trp18 of Smad2. We also observed a novel, so far unidentified modification at Tyr128 and Tyr151. Our observations open for further exploration of biological importance of the detected PTMs.
Generation of a model colon cancer stem cell system provides novel therapeutic opportunities (2007)

A99 Increasing evidence suggests that tumors depend on a subpopulation of cells termed cancer stem cells (CSCs) for tumor initiation and resistance to therapeutic intervention. Targeting the elimination of cancer stem cells therefore presents an opportunity for the development of more effective cancer treatments. A significant obstacle to characterizing cancer stem cells however is the limited ability to expand sufficient clonal populations for phenotypic characterization. Previously it has been demonstrated that CSC populations can be isolated and expanded as 3D tumorospheres from glioblastoma (Bao et al., Nature. 2006; 444:756) and melanoma (Fang et al., Cancer Research, 2005; 65:9328). More recently, CSC populations from colon carcinoma have been isolated based on their expression of the stem cell marker CD133 and expanded as 3D tumorospheres (Ricci-Vitiani et al., Nature 2007; 445:106). Here, we independently demonstrate isolation of tumorospheres from nine out of thirteen surgically resected colon tumor specimens of varying pathology stage and confirm that spheroid formation resides within the CD133 expressing population. Prolonged culturing of tumorospheres in an undifferentiated state was achieved for 3 independent colon cancer specimens with one in culture for over 22 months showing no notable senescence but retaining the ability to self-renew and differentiate towards an adherent epitheloid morphology. The long term spheroid cultures grow in an anchorage independent manner indicating their tumorogenic capacity. Expression of the stem cell markers nestin, BMI-1 and mushahsi-1 support their use as a model for stem cells. Significantly, they also displayed resistance to the growth inhibititory and apoptotic effects mediated by the chemotherapeutic irinotecan. To further characterize the tumorospheres, cell surface proteins were captured and subjected to LC-MS based quantitative proteomic analyses revealing enriched expression of CD133 and CD44. Taken together the characteristics of the expanded CD133 expressing colon cancer tumorospheres isolated suggest they have the potential to serve as a novel model system in which to identify and characterize treatments for colorectal cancer that are capable of targeting cancer stem cells.
Linear Monodisperse π-Conjugated Oligomers: Model Compounds for Polymers and More (1999)

The development of structure-property relationships for monodisperse oligomers has been extremely useful to rationalize the properties of high molecular weight linear π-conjugated polymers. A great variety of spectacular molecular architecture has been generated, culminating in the recent preparation of molecular wires such as 1 with lengths exceeding 10 nm that have potential applications in molecular electronics.
Supplementary Information Figure S2 from Dissecting Therapeutic Resistance to ERK Inhibition (2023)

&lt;p&gt;Maximal Velocity and Km values&lt;/p&gt;
The effects of predator odor (TMT) exposure and mGlu 3 NAM pretreatment on lasting behavioral and molecular adaptations in the insular cortex and BNST (2021)

Abstract A stressor can trigger adaptations that contribute to neuropsychiatric disorders. Predator odor (TMT) exposure is an innate stressor that produces lasting adaptations. TMT exposure may activate metabotropic glutamate receptor 3 (mGlu 3 ), triggering excitatory corticolimbic adaptations that underlie behavioral changes. To evaluate functional involvement, the mGlu 3 negative allosteric modulator (NAM, VU6010572; 3 mg/kg, i.p.) was administered before TMT exposure in male, Long Evans rats. Two weeks after stressor, rats underwent behavioral testing (context re-exposure, zero maze and acoustic startle response) followed by RT-PCR gene expression in the insular cortex and BNST. During the TMT exposure, rats displayed stress-reactive behaviors that were not affected by the VU6010572. During the context re-exposure, prior TMT exposure and VU6010572 pretreatment both produced a hyperactive response. TMT exposure did not affect zero maze or ASR measures, but VU6010572 increased time spent in the open arms and habituation to ASR, indicating anxiolytic-like effects. In the insular cortex, TMT exposure resulted in excitatory adaptations as shown by increased expression of mGlu ( Grm3, Grm5 ), NMDA ( GriN2A, GriN2B, GriN2C, GriN3A, GriN3B ) and AMPA ( GriA3 ) receptor transcripts. Interestingly, mGlu 3 signaling during stressor mediated GriN3B upregulation. Stress reactivity during TMT exposure was associated with Grm5, GriN2A, GriN2C , and GriA3 upregulation in the insular cortex and context re-exposure reactivity in the TMT/vehicle, but not the TMT/mGlu 3 NAM group. In the BNST, GriN2A, GriN2B and GriN3B were increased by VU6010572, but TMT prevented these effects. These data demonstrate that mGlu 3 signaling contributes to the lasting behavioral and molecular adaptations of predator odor stressor.
Verifying a signature architecture: a comparative case study (2007)

Abstract We report on a case study in applying different formal methods to model and verify an architecture for administrating digital signatures. The architecture comprises several concurrently executing systems that authenticate users and generate and store digital signatures by passing security relevant data through a tightly controlled interface. The architecture is interesting from a formal-methods perspective as it involves complex operations on data as well as process coordination and hence is a candidate for both data-oriented and process-oriented formal methods. We have built and verified two models of the signature architecture using two representative formal methods. In the first, we specify a data model of the architecture in Z that we extend to a trace model and interactively verify by theorem proving. In the second, we model the architecture as a system of communicating processes that we verify by finite-state model checking. We provide a detailed comparison of these two different approaches to formalization (infinite state with rich data types versus finite state) and verification (theorem proving versus model checking). Contrary to common belief, our case study suggests that Z is well suited for temporal reasoning about process models with complex operations on data. Moreover, our comparison highlights the advantages of proving theorems about such models and provides evidence that, in the hands of an experienced user, theorem proving may be neither substantially more time-consuming nor more complex than model checking.
Normalized Coordinate Equations and an Energy Method for Predicting Natural Curved-Fold Configurations (2019)

Abstract Of the many valid configurations that a curved fold may assume, it is of particular interest to identify natural—or lowest energy—configurations that physical models will preferentially assume. We present normalized coordinate equations—equations that relate fold surface properties to their edge of regression—to simplify curved-fold relationships. An energy method based on these normalized coordinate equations is developed to identify natural configurations of general curved folds. While it has been noted that natural configurations have nearly planar creases for curved folds, we show that nonplanar behavior near the crease ends substantially reduces the energy of a fold.
Adhesion between template materials and UV-cured nanoimprint resists (2006)

The origins of defects in lithographic stencils fabricated by the UV-cure nanoimprint technique include fundamental surface interactions between template and resist in addition to the presence of particles and contaminants. Repeated, molecularly clean separations of the template from the newly cured resist is a requirement, yet rather little is understood about the separation process or underlying interfacial physics and chemistry. We have investigated the chemical and physical interactions of several model acrylate nanoimprint resist formulations cured in contact with clean and release-treated quartz surfaces, then separated from them. The results show that fracture energies are resist formulation-dependent, that the resist-release layer systems studied are not chemically stable and that release process is more complex than simple fracture at a glass-organic interface.
Chiral Memory via Chiral Amplification and Selective Depolymerization of Porphyrin Aggregates (2010)

Chiral memory at the supramolecular level is obtained via a new approach using chiral Zn porphrins and achiral Cu porphyrins. In a "sergeant-and-soldiers" experiment, the Zn "sergeant" transfers its own chirality to Cu "soldiers" and, after chiral amplification, the "sergeant" is removed from the coaggregates by axial ligation with a Lewis base. After this extraction, the preferred helicity observed for the aggregates containing achiral Cu porphyrins reveals a chiral memory effect that is stable and can be erased and partially restored upon subsequent heating and cooling.
ChemInform Abstract: EPOXYANNULATION. II. CYCLIZATION OF Ω‐KETOSULFONIUM SALTS (1981)

Abstract Aus dem Ketoester (I) erhält man bei der Alkylierung mit (II) und Hydrolyse das Substitutionsprodukt (III), das über ein Ylid zu den stereoisomeren Epoxiden (IV) führt.
Mechanistic insights into oxidosqualene cyclizations through homology modeling (2003)

2,3-Oxidosqualene cyclases (OSC) are key enzymes in sterol biosynthesis. They catalyze the stereoselective cyclization and skeletal rearrangement of (3S)-2,3-oxidosqualene to lanosterol in mammals and fungi and to cycloartenol in algae and higher plants. Sequence information and proposed mechanism of 2,3-oxidosqualene cyclases are closely related to those of squalene-hopene cyclases (SHC), which represent functional analogs of OSCs in bacteria. SHCs catalyze the cationic cyclization cascade converting the linear triterpene squalene to fused ring compounds called hopanoids. High stereoselectivity and precision of the skeletal rearrangements has aroused the interest of researchers for nearly half a century, and valuable data on studying mechanistic details in the complex enzyme-catalyzed cyclization cascade has been collected. Today, interest in cyclases is still unbroken, because OSCs became targets for the development of antifungal and hypocholesterolemic drugs. However, due to the large size and membrane-bound nature of OSCs, three-dimensional structural information is still not available, thus preventing a complete understanding of the atomic details of the catalytic mechanism. In this work, we discuss results gained from homology modeling of human OSC based on structural information of SHC from Alicyclobacillus acidocaldarius and propose a structural model of human OSC. The model is in accordance with previously performed experimental studies with mechanism-based suicide inhibitors and mutagenesis experiments with altered activity and product specificity. Structural insight should strongly stimulate structure-based design of antifungal or cholesterol-lowering drugs.
The Variation of Radiation Transmittance by the cw 1.07 ㎛ Fiber Laser and Water Aerosol Interaction (2012)

Among the atmospheric effect of laser propagation, the variations of the radiation transmittance by water aerosol evaporation have quantitatively been investigated. When the aerosol was exposed by a 1.07 <TEX>${\mu}m$</TEX> cw fiber laser, the increased amount of the transmittance variation was a maximum of 19.1% and the volume concentration variation of aerosol was observed as an increasing of laser intensity. Also, significant irregularity of refractive index was not found in the heated area during the continuous laser heating.
Modifiable Factors Associated with Achievement of High-Volume Post-Dilution Hemodiafiltration: Results from An International Study (2015)

Dialysis center policy in terms of blood flow, treatment time, filter size, and perhaps even hemoglobin targets plays a key role in achieving high-volume HDF. All of these are modifiable factors that can help in prescribing an optimal combination of dialyzer size, achievable blood flows, and treatment times.
Monte Carlo simulations of liquid acetonitrile with a three-site model (1988)

A simple intermolecular potential function has been devised to yield good thermodynamic and structural results for liquid acetonitrile The function was tested in Monte Carlo statistical mechanics simulations for the liquid at temperatures of 25°C and 70°C at 1 atm. The average errors in the computed densities and heats of vaporization are 1–2 per cent. The structural results are presented by means of radial distribution functions and dipole-dipole correlation functions, and compared with prior findings. In addition, the importance of the electrostatic interactions in determining the liquid's structure is illustrated by the results of a simulation at 25°C with the partial charges set to zero.
Polymer-polymer interfacial slip by direct visualization and by stress reduction (2010)

We studied polymer-polymer interfacial slip in bilayer films of highly immiscible (interaction parameter, χ≅0.1) polyethylene and fluoropolymer from medium to higher shear stresses (10–200 kPa) using both visualization and stress reduction. We found good agreement between results from the two methods as well as with previous studies using multilayers by Lee et al. [J. Rheol. 53, 893–915 (2009)] and visualization of flow in a transparent capillary by Migler et al. [J. Rheol. 45, 565–581 (2001)]. We observed two power-law regions: Vslip∝τ6.2 with a transition to Vslip∝τ1.8 at 50 kPa. This is in contrast to the theory of Brochard-Wyart and de Gennes [C. R. Acad. Sci., Ser. II: Mec., Phys., Chim., Sci. Terre Univers 317, 13–17 (1993)], which predicts a transition from infinite slope to a slope of one at a critical stress.
Diversity of Helicobacter pylori vacA and cagA Genes and Relationship to VacA and CagA Protein Expression, Cytotoxin Production, and Associated Diseases (1998)

The vacuolating cytotoxin and the cytotoxin-associated protein, encoded by vacA and cagA, respectively, are important virulence determinants of Helicobacter pylori. Sixty-five H. pylori strains were isolated from dyspeptic patients (19 with peptic ulcer disease, 43 with chronic gastritis, and 3 with gastric cancer) and studied for differences in the vacA and cagA genes and their relationship to VacA and CagA expression, cytotoxin activity, and the clinical outcome of infection. By PCR, fifty-four (83.1%) of 65 strains had the vacA signal sequence genotype s1 and only 10 (15.4%) had the type s2. After primer modification, the vacA middle-region types m1 and m2 were detected in 24 (36.9%) and 41 (63.1%) strains, respectively. The combinations s1-m2 (31 [47.7%]) and s1-m1 (23 [35.4%]) occurred more frequently than s2-m2 (10 [15.4%]) (P = 0.01). No strain with the combination s2-m1 was found. All 19 patients with peptic ulcers harbored type s1 strains, in contrast to 32 (74.4%) of 43 patients with gastritis (P = 0.02). The vacA genotype s1 was associated with the presence of cagA (P < 0.0001), VacA expression (P < 0.0001), and cytotoxin activity (P = 0.003). The cagA gene was detectable in 48 (73.8%) of 65 isolates and present in 16 (84.2%) of 19 ulcer patients and 29 (67.4%) of 43 patients with gastritis (P = 0.17). The vacA genotypes of German H. pylori isolates are identical to those previously reported. H. pylori strains of vacA type s1 are associated with the occurrence of peptic ulceration and the presence of cagA, cytotoxin activity, and VacA expression.
Wafer-scale functional circuits based on two dimensional semiconductors with fabrication optimized by machine learning (2021)

Triggered by the pioneering research on graphene, the family of two-dimensional layered materials (2DLMs) has been investigated for more than a decade, and appealing functionalities have been demonstrated. However, there are still challenges inhibiting high-quality growth and circuit-level integration, and results from previous studies are still far from complying with industrial standards. Here, we overcome these challenges by utilizing machine-learning (ML) algorithms to evaluate key process parameters that impact the electrical characteristics of MoS<sub>2</sub> top-gated field-effect transistors (FETs). The wafer-scale fabrication processes are then guided by ML combined with grid searching to co-optimize device performance, including mobility, threshold voltage and subthreshold swing. A 62-level SPICE modeling was implemented for MoS<sub>2</sub> FETs and further used to construct functional digital, analog, and photodetection circuits. Finally, we present wafer-scale test FET arrays and a 4-bit full adder employing industry-standard design flows and processes. Taken together, these results experimentally validate the application potential of ML-assisted fabrication optimization for beyond-silicon electronic materials.