gebhart/patrepeval huggingface dataset:
Central Role of Endogenous Gamma Interferon in Protective Immunity against Blood-StagePlasmodium chabaudiAS Infection (2000)

The role of endogenous gamma interferon (IFN-gamma) in protective immunity against blood-stage Plasmodium chabaudi AS malaria was studied using IFN-gamma gene knockout (GKO) and wild-type (WT) C57BL/6 mice. Following infection with 10(6) parasitized erythrocytes, GKO mice developed significantly higher parasitemia during acute infection than WT mice and had severe mortality. In infected GKO mice, production of interleukin 12 (IL-12) p70 and tumor necrosis factor alpha in vivo and IL-12 p70 in vitro by splenic macrophages was significantly reduced compared to that in WT mice and the enhanced nitric oxide (NO) production observed in infected WT mice was completely absent. WT and GKO mice had comparable numbers of total nucleated spleen cells and B220(+) and Mac-1(+) spleen cells both before and after infection. Infected WT mice, however, had significantly more F4/80(+), NK1.1(+), and F4/80(+)Ia(+) spleen cells than infected GKO mice; male WT had more CD3(+) cells than male GKO mice. In comparison with those from WT mice, splenocytes from infected GKO mice had significantly higher proliferation in vitro in response to parasite antigen or concanavalin A stimulation and produced significantly higher levels of IL-10 in response to parasite antigen. Infected WT mice produced more parasite-specific immunoglobulin M (IgM), IgG2a, and IgG3 and less IgG1 than GKO mice. Significant gender differences in both GKO and WT mice in peak parasitemia levels, mortality, phenotypes of spleen cells, and proliferation of and cytokine production by splenocytes in vitro were apparent during infection. These results thus provide unequivocal evidence for the central role of endogenous IFN-gamma in the development of protective immunity against blood-stage P. chabaudi AS.
Predicting Silk Fiber Mechanical Properties through Multiscale Simulation and Protein Design (2017)

Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties. Model outcomes are validated experimentally with the genetic design of protein polymers that match the simulation structures, fiber fabrication from these polymers, and mechanical testing of these fibers. Through iterative feedback between computation, genetic synthesis, and fiber mechanical testing, this protocol will enable a priori prediction capability of recombinant material mechanical properties via insights from the resulting molecular architecture of the fiber network based entirely on the initial protein monomer composition. This style of protocol may be applied to other fields where a research team seeks to design a biomaterial with biomedical application-specific properties. This protocol highlights when and how the three research groups (simulation, synthesis, and engineering) should be interacting to arrive at the most effective method for predictive design of their material. Keywords: computational modeling; genetic synthesis; recombinant silk; spinning
Making smart drugs smarter: The importance of linker chemistry in targeted drug delivery (2020)

Smart drugs, such as antibody-drug conjugates, for targeted therapy rely on the ability to deliver a warhead to the desired location and to achieve activation at the same site. Thus, designing a smart drug often requires proper linker chemistry for tethering the warhead with a vehicle in such a way that either allows the active drug to retain its potency while being tethered or ensures release and thus activation at the desired location. Recent years have seen much progress in the design of new linker activation strategies. Herein, we review the recent development of chemical strategies used to link the warhead with a delivery vehicle for preferential cleavage at the desired sites.
An integrated CMOS distributed amplifier utilizing packaging inductance (1997)

An integrated CMOS distributed amplifier is presented. The required inductance needed for the distributed waveguide structure is realized by the parasitic packaging inductance of a plastic surface-mount package. A fully packaged three-stage distributed amplifier fabricated in a 0.8-/spl mu/m CMOS process is presented. The distributed amplifier has a unity gain cutoff frequency of 4.7 GHz, a gain of 5 dB, with a gain flatness of /spl plusmn/1.2 dB over the 300-kHz to 3-GHz band. At a frequency of 2 GHz the amplifier has an input referred third-order intercept point of +15 dBm and an input referred 1-dB compression point of +7 dBm. The amplifier consumes 18 mA from a 3.0-V supply. The distributed amplifier is matched to 50 /spl Omega/ at the input and output and has a maximum input voltage standing-wave ratio (VSWR) of 1.7:1, and a maximum output VSWR of 1.3:1 over the 300 kHz to 3 GHz band. The amplifier has a noise figure of 5.1 dB at 2 GHz.
Prospective Multicenter Cohort Study to Refine Management Recommendations for Women at Elevated Familial Risk of Breast Cancer: The EVA Trial (2010)

In women at elevated familial risk, quality-assured MRI screening shifts the distribution of screen-detected breast cancers toward the preinvasive stage. In women undergoing quality-assured MRI annually, neither mammography, nor annual or half-yearly ultrasound or CBE will add to the cancer yield achieved by MRI alone.
Isolectins from Solanum tuberosum with Different Detailed Carbohydrate Binding Specificities: Unexpected Recognition of Lactosylceramide by N-Acetyllactosamine-Binding Lectins (2000)

Glycosphingolipid recognition by two isolectins from Solanum tuberosum was compared by the chromatogram binding assay. One lectin (PL-I) was isolated from potato tubers by affinity chromatography, and identified by MALDI-TOF mass spectrometry as a homodimer with a subunit molecular mass of 63,000. The other (PL-II) was a commercial lectin, characterized as two homodimeric isolectins with subunit molecular masses of 52,000 and 55,000, respectively. Both lectins recognized N-acetyllactosamine-containing glycosphingolipids, but the fine details of their carbohydrate binding specificities differed. PL-II preferentially bound to glycosphingolipids with N-acetyllactosamine branches, as Galbeta4GlcNAcbeta6(Galbeta4GlcNAcbeta3)Galbeta4Glcbeta1C er. PL-I also recognized this glycosphingolipid, but bound equally well to the linear glycosphingolipid Galbeta4GlcNAcbeta3Galbeta4GlcNAcbeta3Galbeta4Glcbeta1Cer. Neolactotetraosylceramide and the B5 pentaglycosylceramide were also bound by PL-I, while other glycosphingolipids with only one N-acetyllactosamine unit were non-binding. Surprisingly, both lectins also bound to lactosylceramide, with an absolute requirement for sphingosine and non-hydroxy fatty acids. The inhibition of binding to both lactosylceramide and N-acetyllactosamine-containing glycosphingolipids by N-acetylchitotetraose suggests that lactosylceramide is also accomodated within the N-acetylchitotetraose/N-acetyllactosamine-binding sites of the lectins. Through docking of glycosphingolipids onto a three-dimensional model of the PL-I hevein binding domain, a Galbeta4GlcNAcbeta3Galbeta4 binding epitope was defined. Furthermore, direct involvement of the ceramide in the binding of lactosylceramide was suggested.
Solid Forms (2000)

This chapter contains sections titled: Powders and Powder Mixtures Agglomerates, Granules Preparation and Properties of Instant Products Microencapsulation
Critique of 'An Analysis of the Blast Overpressure Study Data Comparing Three Exposure Criteria' by Murphy Khan and Shaw (2010)

Abstract : Murphy et al. analyzed the performance of MIL-STD-1747D, LAEQ8, and the Auditory Hazard Assessment Algorithm for Humans (AHAAH)model as they predicted outcomes on the Albuquerque studies (AS) data set. Unfortunately, they erred in several invalidating ways. First,they overlooked underlying nonlinearities in the hearing protector (which rendered the AS data set unique, the use of MIL-STD-1474D invalid, and the LAEQ8 calculations useless outside the data set). They overlooked the nonlinear conductive path of the ear that, at the very high intensities, greatly affected the energy reaching the cochlea (which implies that their LAEQ8 analyses measured under the muff cannot be usefully extrapolated outside the data set). Their analysis of LAEQ8 under the protector did establish that a criterion level of 110-dB LAEQ8 fits the data, but they failed to comment on the discrepancy between this level and the 85-dB LAEQ8 criterion that is traditionally used. Further, they misapplied the AHAAH model in using the unwarned calculation and overlooked the model's capacity to predict the effect on different percentiles of the population. Their analysis indicated that the warned calculation with the AHAAH model did rank hazard acceptably for the 95th percentile ear, and we note that it did so for small arms fire as well, all without adjustment. More research in the pressure regime between 115 and 160 dB is needed for the development of a comprehensive damage risk criterion for intense noise.
Data from Characterization of an Abiraterone Ultraresponsive Phenotype in Castration-Resistant Prostate Cancer Patient-Derived Xenografts (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; To identify the molecular signature associated with abiraterone acetate (AA) response and mechanisms underlying AA resistance in castration-resistant prostate cancer patient-derived xenografts (PDXs).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; SCID mice bearing LuCaP 136CR, 77CR, 96CR, and 35CR PDXs were treated with AA. Tumor volume and prostate-specific antigen were monitored, and tumors were harvested 7 days after treatment or at end of study for gene expression and immunohistochemical studies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Three phenotypic groups were observed based on AA response. An ultraresponsive phenotype was identified in LuCaP 136CR with significant inhibition of tumor progression and increased survival, intermediate responders LuCaP 77CR and LuCaP 96CR with a modest tumor inhibition and survival benefit, and LuCaP 35CR with minimal tumor inhibition and no survival benefit upon AA treatment. We identified a molecular signature of secreted proteins associated with the AA ultraresponsive phenotype. Upon resistance, AA ultraresponder LuCaP 136CR displayed reduced androgen receptor (AR) signaling and sustainably low nuclear glucocorticoid receptor (nGR) localization, accompanied by steroid metabolism alteration and epithelial–mesenchymal transition phenotype enrichment with increased expression of NF-κB–regulated genes; intermediate and minimal responders maintained sustained AR signaling and increased tumoral nGR localization.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; We identified a molecular signature of secreted proteins associated with AA ultraresponsiveness and sustained AR/GR signaling upon AA resistance in intermediate or minimal responders. These data will inform development of noninvasive biomarkers predicting AA response and suggest that further inhibition along the AR/GR signaling axis may be effective only in AA-resistant patients who are intermediate or minimal responders. These findings require verification in prospective clinical trials. &lt;i&gt;Clin Cancer Res; 23(9); 2301–12. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Molecular Analysis of Microtubule-Associated Protein-2 Kinase cDNA from Mouse and Rat Brain (1991)

We have isolated and characterized brain cDNA clones encoding microtubule-associated protein-2 (MAP-2) kinase for rat (rMNK1) and mouse (mMNK1). The nucleotide sequences diverged by only 5% whereas the amino acid sequences were identical except for one conservative residue change. Conservation of the expressed sequence extended into other mammalian species. These findings constitute the first demonstration of a strict evolutionary conservation of MAP-2 kinase. Genomic restriction patterns revealed a single MAP-2 kinase gene that shares homology with other genomic sequences. The 3' terminal half of the gene appears to be encoded by four exons. rMNK1 and mMNK1 differed from a recently reported MAP-2 kinase cDNA, termed ERK1, because of a nonconservative change in position 82, from Gly in ERK1 to Arg in rMNK1. The rMNK1 gene was found to be expressed mainly as a 1.8-kb transcript that was highest in brain and in lung. In contrast to ERK1, rMNK1 showed two equally prominent mRNA species in liver, at 1.8 kb and 5 kb, which imply differential processing of the primary transcript. Results derived from the immunological screening of an expression library showed that MAP-2 kinase might share epitopes with two prominent protein kinase C substrates, MARCKS (an 80-kD protein kinase C substrate) and GAP-43, suggesting the possibility that MAP-2 kinase could interact with kinase C.
Effect of probenecid on the formation and elimination of acyl glucuronides: Studies with zomepirac (1985)

When 100 mg oral zomepirac was taken with 500 mg b.i.d. oral probenecid by six healthy subjects, the disposition of zomepirac was markedly altered. Probenecid decreased total plasma clearance of zomepirac by 64%, which resulted in an increase in bioavailability from 0.55 without probenecid to 0.84 when given concurrently. The apparent metabolic clearance of zomepirac to form zomepirac acyl glucuronide was reduced 71% and zomepirac renal clearance, a minor elimination route, was reduced by 79%. When assayed by a method that prevents degradation of the labile acyl glucuronide, zomepirac glucuronide concentrations in plasma were comparable to those of zomepirac. Probenecid decreased the renal clearance of zomepirac glucuronide by 72%, which, together with the increased zomepirac levels, resulted in a 2.8-fold increase in the AUC of the conjugate. Urinary excretion of zomepirac glucuronide was reduced from 72% to 58% of the dose, but the excretion of free zomepirac was unchanged at 5% of the dose. The ratio of the total clearance/bioavailability of zomepirac in control subjects was 682 +/- 246 ml/min, which is double the value reported in previous studies of zomepirac disposition. We believe that this difference is due to degradation of the unstable zomepirac acyl glucuronide in the previous analytic methodologies used. Qualitatively, the effects of probenecid on zomepirac disposition are similar to those previously reported for other drugs of this class that are metabolized to acyl glucuronides. However, zomepirac appears unusual in that significant levels of its acyl glucuronide metabolite are found in vivo.
The familial association between cigarette smoking and ADHD: A study of clinically referred girls with and without ADHD, and their families (2008)

Attention-deficit/hyperactivity disorder (ADHD) is a strong risk factor for smoking. Since both ADHD and smoking are familial disorders, one way to further our understanding of this association is to examine the familial relationship between them. Our aim was to evaluate the familial association between ADHD and smoking in families ascertained from girls with and without ADHD. Subjects were derived from a longitudinal case-control family study of girls with (n = 140) and without (n = 122) ADHD ascertained from pediatric and psychiatric clinics, and their biological first-degree relatives. Diagnoses of ADHD and smoking (i.e., full or subthreshold nicotine dependence) were made with structured psychiatric interviews. We stratified the relatives into four groups based on probands' ADHD and smoking status: (1) relatives of controls without smoking (probands n = 100, relatives n = 317), (2) relatives of controls with smoking (probands n = 22, relatives n = 71), (3) relatives of ADHD girls without smoking (probands n = 100, relatives n = 320), and (4) relatives of ADHD girls with smoking (probands n = 39, relatives n = 133). We compared the rates of ADHD and smoking across the four relative groups using survival analysis. ADHD in the proband increased the risk for ADHD in the relatives irrespective of probands' smoking and smoking in the proband increased the risk for smoking in the relatives irrespective of probands' ADHD status. Furthermore, we found statistically significant evidence for cosegregation of smoking and ADHD, suggesting that the two disorders are transmitted together through families more often than expected by chance. These findings support the hypothesis that the combination of ADHD and smoking comprises an etiologically distinct familial subtype of ADHD in girls.
Enterovirus Receptors and Entry (2017)

This book represents a comprehensive tour of the current most important enterovirus research. Topics covered include viral entry and the hijacking of host functions; the dynamic analysis of ever-evolving virus genomes; the cellular membrane changes promoting virus assembly and release. A must-read for anyone with an interest in this family of viruses.
Studies on linear aditivity of physical values under three-dimensionally stressed fatigue. (1989)

粒子複合加硫物の三次元応力疲労において, 定応力連続疲労とステップ疲労におけるゴム分子鎖の運動性, 構造間相互作用による弱物理結合(塑性要素), 弾性率及びその熱力学的構成, 構造異方性などに関する諸物性値の変化について検討し, これらの諸物性値はいずれも線形加算性が成立し, ステップ応力疲労における時間は, 次式に示す等価疲労時間t(σ0)により定応力連続疲労に変換できることを実験的に確認した.t(σ0)=∑i[∑jexp{(1-ai)U0-α(σ20-ai(•σ2i)/kT0}•_??_tij]ai=Ti/T0}ここに, σ0, T0は基準応力, 基準温度, σi, _??_tij, Tiはステップ応力疲労における負荷応力, 負荷時間及び温度, k, αはボルツマン定数と定数.
An alternative ionospheric correction algorithm for satellite-based augmentation systems in low-latitude region (2003)

In this paper, we use data from the South American region to perform a quantitative assessment of WAAS-type ionospheric correction algorithms in this region.
SOFC System for Battery Electric Vehicle Range Extension: Results of the First Half of the Mestrex Project (2017)

An SOFC system has been specially designed for a fuel mixture containing water and ethanol. Targets for the system include 5kW Net power output, a 50% net APU efficiency and the system should deliver full power within 30 minutes. In order to reach these targets AVL-List GmbH has developed novel technological solutions that have been integrated into a test stand system. Special metal supported stacks are being developed by Plansee that allow a rapid start and high electrical performance and efficiency. Initial results from all partners are very promising, as a step towards the final goal of a feasible SOFC system integrated into a roadworthy vehicle.
Energy-Efficient Massive MIMO for Federated Learning: Transmission Designs and Resource Allocations (2022)

This work proposes novel synchronous, asynchronous, and session-based designs for energy-efficient massive multiple-input multiple-output networks to support federated learning (FL). The synchronous design relies on strict synchronization among users when executing each FL communication round, while the asynchronous design allows more flexibility for users to save energy by using lower computing frequencies. The session-based design splits the downlink and uplink phases in each FL communication round into separate sessions. In this design, we assign users such that one of the participating users in each session finishes its transmission and does not join the next session. As such, more power and degrees of freedom will be allocated to unfinished users, resulting in higher rates, lower transmission times, and hence, higher energy efficiency. In all three designs, we use zero-forcing processing for both uplink and downlink, and develop algorithms that optimize user assignment, time allocation, power, and computing frequencies to minimize the energy consumption at the base station and users, while guaranteeing a predefined maximum execution time of each FL communication round.
Combinatorial CAR design improves target restriction (2020)

Abstract CAR T cells targeting the B-lymphocyte antigen CD19 have led to remarkable clinical results in B-cell leukemia and lymphoma, but eliminate all B-lineage cells, leading to increased susceptibility to severe infections. As malignant B cells will express either immunoglobulin (Ig) light chain κ or λ, we designed a second-generation CAR targeting Igκ, IGK CAR. This construct demonstrated high target specificity, but displayed reduced efficacy in the presence of serum IgG. Since CD19 CAR is insensitive to serum IgG, we designed various combinatorial CAR constructs in order to maintain the CD19 CAR T cell efficacy, but with IGK CAR target selectivity. The Kz-19BB design, combining CD19 CAR containing a 4-1BB co-stimulatory domain with an IGK CAR containing a CD3zeta stimulatory domain, maintained the target specificity of IgK CAR and was resistant to the presence of soluble IgG. Our results demonstrate that a combinatorial CAR approach can improve target selectivity and efficacy.
Correction: Combined Analysis of Murine and Human Microarrays and ChIP Analysis Reveals Genes Associated with the Ability of MYC To Maintain Tumorigenesis (2013)

The MYC oncogene has been implicated in the regulation of up to thousands of genes involved in many cellular programs including proliferation, growth, differentiation, self-renewal, and apoptosis. MYC is thought to induce cancer through an exaggerated effect on these physiologic programs. Which of these genes are responsible for the ability of MYC to initiate and/or maintain tumorigenesis is not clear. Previously, we have shown that upon brief MYC inactivation, some tumors undergo sustained regression. Here we demonstrate that upon MYC inactivation there are global permanent changes in gene expression detected by microarray analysis. By applying StepMiner analysis, we identified genes whose expression most strongly correlated with the ability of MYC to induce a neoplastic state. Notably, genes were identified that exhibited permanent changes in mRNA expression upon MYC inactivation. Importantly, permanent changes in gene expression could be shown by chromatin immunoprecipitation (ChIP) to be associated with permanent changes in the ability of MYC to bind to the promoter regions. Our list of candidate genes associated with tumor maintenance was further refined by comparing our analysis with other published results to generate a gene signature associated with MYC-induced tumorigenesis in mice.
Deriving the multiplicative algebraic reconstruction algorithm (MART) by the method of convex projection (POCS) (1993)

It is shown that the MART (multiplicative algebraic reconstruction technique) algorithm can be derived by POCS. This gives MART a new theoretical interpretation and a proof of convergence to a stable solution even when other convex constraints are introduced. However, MART, as a multiplicative algorithm, depends on the initial solution. It is noted that, far from being a flaw, this property can be used to introduce further a priori knowledge about the image to be reconstructed, to maximize the entropy, to keep the ratio between the regions of the original image constant, or to set to zero the area outside the reconstruction volume. MART should be preferred to MENT (a maximum entropy algorithm) for entropy maximization, for it performs as well but is much faster. ART is much less influenced by the initial solution than MART.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>