gebhart/patrepeval huggingface dataset:
Treatment of severe acute respiratory syndrome with convalescent plasma. (2003)

In March 2003, an outbreak of severe acute respiratory syndrome started in Hong Kong. A 57-year-old woman had a typical presentation, including fever, non-productive cough, malaise, lymphopenia, and raised liver aminotransferases. The clinical course and successful treatment with convalescent plasma, ribavirin, and corticosteroids are discussed.
Lower power interstitial laser photocoagulation in rat liver: importance of fiber type, laser wavelength, and tissue charring (1993)

To evaluate whether the size of the tissue necrosis achieved by interstitial laser photocoagulation (ILP) is dependent on the fiber core diameter, the fiber cladding, and the laser wavelength used. Methods: Forty six rats were anaesthetized and their livers exposed at laparotomy. A single bare fiber was inserted interstitially into the liver which was then irradiated at 2 W for 100 s or 500 s. Four fibers were used: 0.2 mm and 0.4 mm all silica fibers had their buffer coats/jackets stripped off the distal 3 mm, leaving the cladding intact; 0.2 mm and 0.4 mm plastic clad fibers had their buffer coats/jackets and cladding stripped off the distal 3 mm. A 1064 nm Nd:YAG and an 805 nm diode laser were used. One day after ILP the rats were sacrificed and measurements made of the size of necrosis and of any charring. Results: 1. There was no difference in the size of necrosis from a 0.2 mm or 0.4 mm fiber. 2. Larger areas of necrosis and greater charring were produced with the plastic clad fibers. 3. The 805 nm diode laser gave the largest necrotic size and the greatest charring for a given energy. 4. There was a positive correlation between the degree of charring and the size of the necrosis.
Brillouin instantaneous frequency measurement with an arbitrary response for potential real-time implementation (2019)

We demonstrate an arbitrary-response Brillouin instantaneous frequency measurement (IFM) based on the principle of the frequency-to-power mapping in stimulated Brillouin scattering (SBS), which is named Brillouin IFM. The arbitrary response is realized by periodically sweeping the frequency of the local pump lightwave, and the response's amplitude depends on the sweeping slope. The Brillouin IFM is achieved by the control of the sweeping period lower than the double of the flight-of-time in the SBS interaction length. A Costas frequency coded pulse is experimentally measured to verify the feasibility of the proposed Brillouin IFM scheme. The bandwidth of the digital sampling in the scheme is reduced to 50 MHz. The Brillouin IFM range without averaging reaches 6 GHz at Ku band.
Miniaturizing 3D assay for high-throughput drug and genetic screens for small patient-derived tumor samples (Conference Presentation) (2017)

Three-dimensional growth conditions reflect the natural environment of cancer cells and are crucial to be performed at drug screens. We developed a 3D assay for cellular transformation that involves growth in low attachment (GILA) conditions and is strongly correlated with the 50-year old benchmark assay-soft agar. Using GILA, we performed high-throughput screens for drugs and genes that selectively inhibit or increase transformation, but not proliferation. This phenotypic approach is complementary to our genetic approach that utilizes single-cell RNA-sequencing of a patient sample to identify putative oncogenes that confer sensitivity to drugs designed to specifically inhibit the identified oncoprotein. Currently, we are dealing with a big challenge in our field- the limited number of cells that might be extracted from a biopsy. Small patient-derived samples are hard to test in the traditional multiwell plate and it will be helpful to minimize the culture area and the experimental system. We managed to design a suitable microfluidic device for limited number of cells and perform the assay using image analysis. We aim to test drugs on tumor cells, outside of the patient body- and recommend on the ideal treatment that is tailored to the individual. This device will help to minimize biopsy-sampling volumes and minimize interventions in the patient’s tumor.
The ribosome can discriminate the chirality of amino acids within its peptidyl-transferase center (2015)

The cellular translational machinery (TM) synthesizes proteins using exclusively L- or achiral aminoacyl-tRNAs (aa-tRNAs), despite the presence of D-amino acids in nature and their ability to be aminoacylated onto tRNAs by aa-tRNA synthetases. The ubiquity of L-amino acids in proteins has led to the hypothesis that D-amino acids are not substrates for the TM. Supporting this view, protein engineering efforts to incorporate D-amino acids into proteins using the TM have thus far been unsuccessful. Nonetheless, a mechanistic understanding of why D-aa-tRNAs are poor substrates for the TM is lacking. To address this deficiency, we have systematically tested the translation activity of D-aa-tRNAs using a series of biochemical assays. We find that the TM can effectively, albeit slowly, accept D-aa-tRNAs into the ribosomal aa-tRNA binding (A) site, use the A-site D-aa-tRNA as a peptidyl-transfer acceptor, and translocate the resulting peptidyl-D-aa-tRNA into the ribosomal peptidyl-tRNA binding (P) site. During the next round of continuous translation, however, we find that ribosomes carrying a P-site peptidyl-D-aa-tRNA partition into subpopulations that are either translationally arrested or that can continue translating. Consistent with its ability to arrest translation, chemical protection experiments and molecular dynamics simulations show that P site-bound peptidyl-D-aa-tRNA can trap the ribosomal peptidyl-transferase center in a conformation in which peptidyl transfer is impaired. Our results reveal a novel mechanism through which D-aa-tRNAs interfere with translation, provide insight into how the TM might be engineered to use D-aa-tRNAs, and increase our understanding of the physiological role of a widely distributed enzyme that clears D-aa-tRNAs from cells.
Secondary Amine Pendant β-Peptide Polymers Displaying Potent Antibacterial Activity and Promising Therapeutic Potential in Treating MRSA-Induced Wound Infections and Keratitis (2022)

Interest in developing antibacterial polymers as synthetic mimics of host defense peptides (HPDs) has accelerated in recent years to combat antibiotic-resistant bacterial infections. Positively charged moieties are critical in defining the antibacterial activity and eukaryotic toxicity of HDP mimics. Most examples have utilized primary amines or guanidines as the source of positively charged moieties, inspired by the lysine and arginine residues in HDPs. Here, we explore the impact of amine group variation (primary, secondary, or tertiary amine) on the antibacterial performance of HDP-mimicking β-peptide polymers. Our studies show that a secondary ammonium is superior to either a primary ammonium or a tertiary ammonium as the cationic moiety in antibacterial β-peptide polymers. The optimal polymer, a homopolymer bearing secondary amino groups, displays potent antibacterial activity and the highest selectivity (low hemolysis and cytotoxicity). The optimal polymer displays potent activity against antibiotic-resistant bacteria and high therapeutic efficacy in treating MRSA-induced wound infections and keratitis as well as low acute dermal toxicity and low corneal epithelial cytotoxicity. This work suggests that secondary amines may be broadly useful in the design of antibacterial polymers.
Isomorphic A‐Site Substitution on Sillenite‐Type Compounds (2004)

Investigations of A‐site substitution in sillenite‐type compounds showed that only a substituent ion with a lone‐electron pair can be successfully incorporated onto the A‐site in place of Bi 3+ . This is because the stability of sillenite structural polyhedra is conditioned by the presence of a stereochemically active lone‐electron pair. Accordingly, the substitutional experiments combined with an X‐ray diffraction analysis, energy‐ and wavelength‐dispersive microanalysis, and Rietveld refinement showed that Nd 3+ and La 3+ ions, which do not possess a lone‐electron pair, cannot be incorporated into the sillenite‐type structure above the detection limits of the applied analytical techniques. In contrast, the A‐site substitution of Pb 2+ , Tl + , and Sb 3+ ions, which do possess a lone‐electron pair, was experimentally confirmed. Te 4+ also possesses a lone‐electron pair, but the substitutional experiments showed that this ion did not incorporate into the sillenite structure.
Selective Inhibition of EZH2 by EPZ-6438 Leads to Potent Antitumor Activity in EZH2 -Mutant Non-Hodgkin Lymphoma (2014)

Mutations within the catalytic domain of the histone methyltransferase EZH2 have been identified in subsets of patients with non-Hodgkin lymphoma (NHL). These genetic alterations are hypothesized to confer an oncogenic dependency on EZH2 enzymatic activity in these cancers. We have previously reported the discovery of EPZ005678 and EPZ-6438, potent and selective S-adenosyl-methionine-competitive small molecule inhibitors of EZH2. Although both compounds are similar with respect to their mechanism of action and selectivity, EPZ-6438 possesses superior potency and drug-like properties, including good oral bioavailability in animals. Here, we characterize the activity of EPZ-6438 in preclinical models of NHL. EPZ-6438 selectively inhibits intracellular lysine 27 of histone H3 (H3K27) methylation in a concentration- and time-dependent manner in both EZH2 wild-type and mutant lymphoma cells. Inhibition of H3K27 trimethylation (H3K27Me3) leads to selective cell killing of human lymphoma cell lines bearing EZH2 catalytic domain point mutations. Treatment of EZH2-mutant NHL xenograft-bearing mice with EPZ-6438 causes dose-dependent tumor growth inhibition, including complete and sustained tumor regressions with correlative diminution of H3K27Me3 levels in tumors and selected normal tissues. Mice dosed orally with EPZ-6438 for 28 days remained tumor free for up to 63 days after stopping compound treatment in two EZH2-mutant xenograft models. These data confirm the dependency of EZH2-mutant NHL on EZH2 activity and portend the utility of EPZ-6438 as a potential treatment for these genetically defined cancers.
The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance (2016)

The B. tabaci genome contains numerous genetic novelties, including expansions in gene families associated with insecticide resistance, detoxification and virus transmission, as well as numerous horizontally transferred genes from bacteria and fungi. We believe these novelties likely have shaped B. tabaci as a highly invasive polyphagous crop pest and efficient vector of plant viruses. The genome serves as a reference for resolving the B. tabaci cryptic species complex, understanding fundamental biological novelties, and providing valuable genetic information to assist the development of novel strategies for controlling whiteflies and the viruses they transmit.
Determination of elements in river water (2022)

Main text The need for quality assessment of anthropogenic impact on environmental pollution is increasing due to discharge from various industries, the use of chemicals in agriculture and the consumption of fossil fuels. Diminishing resources such as natural waters used for the cultivation of agricultural products, plant and animal habitats are under severe pollution pressure and are at constant risk. Several parameters, such as Pb, Cd, Ni, Hg were listed by Water Framework Directive in Directive (2008/105/EC) in the priority substances. Cadmium and Hg were identified as priority hazardous substances whereas As is an important contaminant for its potential toxicological and carcinogenic effects. An inter-comparison study is organised in EURAMET TC-MC in order to demonstrate the capability participants for measuring five elements in river water. The participants carried out measurements for analytes: Pb, Cd, Ni and As as mandatory elements, and Se as an optional one. Participants were asked to perform the measurements with respect to the protocol provided. To reach the main text of this paper, click on Final Report . Note that this text is that which appears in Appendix B of the BIPM key comparison database https://www.bipm.org/kcdb/ . The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Persistence of the Mini Pivot Shift after Anatomically Placed Anterior Cruciate Ligament Reconstruction (2006)

We hypothesized that traces of pivot-shift instability (a minipivot) would persist after anterior cruciate ligament reconstruction in some knees despite objective restoration of anteroposterior laxity to normal. We tested intact cadaver knees after anterior cruciate ligament transection and then after anatomically placed single-bundle anterior cruciate ligament reconstructions. We measured the rotational laxities and pivot-shift kinematics over a range of graft tensions. Increasing graft tension decreased anteroposterior laxity; anteroposterior laxity was greater than normal at 0 and 10 N tensions but not different than normal at 20 to 60 N tensions. Anterior cruciate ligament deficiency had little effect on rotation laxity, and reconstruction had little effect on rotational laxity, which was not reduced by increasing graft tension. During the pivot-shift test, increasing graft tension reduced the anteroposterior subluxation-reduction events, but tibial rotational was not restored to normal. More sophisticated reconstruction methods may be required to control rotation. Objective restoration of anteroposterior laxity to normal does not necessarily return knee kinematics, especially rotational behavior, to normal.
Experimentally validated multi-step simulation strategy to predict the fatigue crack propagation rate in residual stress fields after laser shock peening (2018)

Laser shock peening (LSP) is a promising technology to retard the fatigue crack propagation (FCP) in metallic lightweight structures. A multi-step simulation strategy to predict FCP in LSP-induced residual stress fields is proposed and applied. The simulation strategy involves an LSP process simulation, a transfer approach to include the plastic strains in a C(T) specimen model to calculate the residual stresses and an FCP simulation to determine the stress intensity factors. The FCP rate is finally determined via FCP equations. The validity of the simulation strategy including the crack driving quantities prediction is experimentally demonstrated by a novel 'simulation' approach.
Numerical investigation on a seismic testing campaign on adjustable pallet rack speed-lock connections (2021)

This paper presents numerical simulations of a suite of cantilever seismic tests of speed-lock connections between beam and upright members of adjustable pallet rack systems. The tested specimens differ in the endplate-to-beam weld beads geometric configuration; the experimental results show that each weld configuration leads to different behavior, significantly affecting the connection capacity and ductility. As a result, the performed numerical simulations aim to better understand and deepen these observations. Special attention is paid to the initial (elastic) behavior of the tested assembly, albeit the stress redistribution after the first yielding has also been studied and found to be relevant. The numerical results are satisfactory compared with the experimental ones, and specific remarks are derived. This work is a part of a broader research effort aimed to improve the dissipative seismic behavior of racks; such research activity involves also upright-base plate connections testing, advanced numerical simulation, and proposal of rack ductility behavior factors.
Long-Term Exposure to Cigarette Smoke Extract Induces Hypomethylation at the RUNX3 and IGF2-H19 Loci in Immortalized Human Urothelial Cells (2013)

Cigarette smoking is the single most important epidemiological risk factor for bladder cancer but it is not known whether exposure of urothelial cells to the systemic soluble contents of cigarette smoke is directly causative to bladder cancer and the associated epigenetic changes such as tumor suppressor gene hypermethylation. We undertook this study to investigate if long-term treatment of human urothelial cells with cigarette smoke extract (CSE) results in tumor suppressor gene hypermethylation, a phenotype that was previously associated with long-term constant CSE treatment of airway epithelial cells. We chronically treated an immortalized human urothelial cell line UROtsa with CSE using a cyclic daily regimen but the cells were cultured in CSE-free medium between daily treatments. Bisulfite sequencing and real-time PCR array-based methylation profiling were employed to evaluate methylation changes at tumor suppressor gene loci in the chronically CSE-treated cells versus the passage-matched untreated control cells. The RUNX3 tumor suppressor gene promoter was hypomethylated with a significant increase in proportion of the completely unmethylated haplotype after the long-term CSE treatment; whereas RUNX3 promoter hypermethylation was previously reported for bladder cancers of smokers. Hypomethylation induced by the long-term CSE treatment was also observed for the IGF2-H19 locus. The methylation status at the PRSS8/prostasin and 16 additional loci however, was unaffected by the chronic CSE treatment. Transient CSE treatment over 1 daily regimen resulted in transcriptional down-regulation of RUNX3 and H19, but only the H19 transcription was down-regulated in the chronically CSE-treated urothelial cells. Transcription of a key enzyme in one-carbon metabolism, dihydrofolate reductase (DHFR) was greatly reduced by the long-term CSE treatment, potentially serving as a mechanism for the hypomethylation phenotype via a reduced supply of methyl donor. In conclusion, chronic cyclic CSE treatment of urothelial cells induced hypomethylation rather than hypermethylation at specific loci.
Positron emission tomographic study of suppression of gray-matter glucose utilization by brain tumors. (1983)

Positron emission tomography (PET) scanning with [18F]-2-fluoro-2-deoxy-D-glucose (FDG) was used to study 59 patients with astrocytomas and three patients with other cerebral mass lesions. Suppression of gray-matter glucose utilization ranging from 8% to 64% (mean, 30%) was seen in 92% of cases. Three categories of suppression were apparent, with the greatest degrees of suppression occurring in edematous gray matter adjacent to mass lesions. Lesser degrees of suppression were noted in nonedematous structures (normal attenuation on computed tomographic scan) adjacent to the lesion. Significant suppression was also present in gray matter spatially remote from but functionally linked to the site of the lesion. This approach may become a useful tool for improved understanding of the clinical presentation of certain pathologic entities and for evaluation of disease progression and response to treatment.
NeuLaw Criminal Record Database (2016)

Traditionally, criminal research on a national scale has relied primarily on the FBI's Uniform Crime Reports (UCR), a tool with several weaknesses: (1) it contains no unique personal identifiers, precluding analysis of re-offense rates, (2) it lacks detail about individual crimes and their outcomes (e.g., number of charges, plea bargains, dispositions, fines, jail sentences), (3) reporting to the UCR is highly variable, so the aggregate statistics cannot be read as a comprehensive picture of crime. An alternative approach to crime record analysis can be pursued by the study of individual court records, housed in hundreds of counties across the United States. However, each jurisdiction employs local laws and sparse, idiosyncratic information management systems, making it prohibitively difficult to compare detailed crime records across time and place.To overcome all these limitations, we have developed the NeuLaw Criminal Record Database (CRD), a rich and growing collection of tens of millions of crime records. The CRD provides an unprecedented level of detail about individual offenders, their crimes, and their interactions with the criminal justice system; additionally, it translates court records into a common framework for cross-jurisdiction comparison. In particular, the database includes anonymized identifiers to enable large-scale exploration of criminal re-offense (recidivism). The CRD is growing monthly; as of this writing it contains 22.5 million records from 1977 to 2014 from Harris County in Texas, New York City, Miami-Dade County in Florida, and the state of New Mexico. The database can enable or enhance many types of research—for example, identification of high-risk offenders, measurement of changes in policing strategies, and quantification of legislative efficacy—thus giving policy makers the best data upon which to base law enforcement decisions.<br>
Synthesis and Carrier Transport Properties of Triarylamine-based Amorphous Polymers for Organic Field-effect Transistors (2009)

Abstract Twenty-three kinds of triarylamine-based polymers, which are a new class of p-type semiconducting materials for organic field-effect transistors (OFETs), were synthesized by Pd-catalyzed amination of the corresponding aryldihalide and arylamine. All triarylamine-based polymers in this study exhibited p-channel behavior in OFETs, and field-effect hole mobilities ranged from 10−6 to 10−3 cm2 V−1 s−1.
Packet Delivery Performance in Dense Wireless Sensor Networks (2003)

Wireless sensor networks promise fine-grain monitoring in a wide variety of environments. Many of these environments (indoor environments or habitats) can be harsh for wireless communication. From a networking perspective, the most basic aspect of wireless communication is the packet delivery performance: the spatio-temporal characteristics of packet loss, and its environmental dependence. These factors will deeply impact the performance of data acquisition from these networks. In this presentation, we report on a systematic medium-scale (up to sixty nodes) measurement of packet delivery in three different environments: an indoor office building, a habitat with moderate foliage, and an open parking lot. Our findings have interesting implications for the design and evaluation of routing and medium-access protocols for sensor networks.
Co-design of power amplifier and narrowband filter using high-Q evanescent-mode cavity resonator as the output matching network (2011)

A unique GaN power amplifier (PA) with an integrated evanescent-mode resonator as its output matching network is presented in this paper. Instead of matching the output of the GaN transistor to 50 Ω and connecting it to a 50-Ω bandpass filter, the GaN is directly integrated with a one-pole filter thus eliminating the conventionally-employed output matching network after the GaN transistor. This leads to a reduced circuit complexity and higher efficiency. The one-pole filter implemented by a strongly-coupled evanescent-mode cavity resonator with an unloaded quality factor of 320 is experimentally presented as a proof-of-concept demonstration. This design yields a very narrowband PA response from 1.24-1.275 GHz (2.8%), which is comparable to the bandwidth of typical communication signals. The PA exhibits a state-of-the-art performance of >; 70% efficiency, >; 10 dB gain, >; 30 dBm output power, and second and third harmonic levels of <; -70 dBc. The presented methodology has the potential to be further extended to a tunable design for multi-band applications.