gebhart/patrepeval huggingface dataset:
A Novel Promoter for Vascular Endothelial Growth Factor Receptor (flt-1) That Confers Endothelial-specific Gene Expression (1995)

The human transmembrane fms-like receptor tyrosine kinase Flt-1 is one of the receptors for vascular endothelial growth factor, a growth factor which induces endothelial proliferation and vascular permeability. Flt-1 is expressed specifically in endothelium and is likely to play a role in tumor angiogenesis and embryonic vascularization. To elucidate the molecular basis for the endothelial specific expression of Flt-1, the promoter region has been isolated and functionally characterized. The promoter region contains a TATA box, a GC-rich region, and putative transcription factor binding elements such as cAMP response element binding protein/activating transcription factor (CREB/ATF) and ets. Adenovirus-mediated transient expression of the flt-1 promoter/luciferase fusion gene in endothelial cells and other cell types demonstrated that a 1-kilobase fragment of the 5'-flanking region of flt-1 is involved in the endothelial-specific expression. A CREB/ATF element was found to be essential for basal transcription of the flt-1 expression. In addition, we also showed that the first intron negatively regulates flt-1 promoter activity. The flt-1 promoter will be useful in functional studies on the regulation of endothelial-specific gene expression and also as a tool in targeting the expression of exogenously introduced genes to the endothelium.
Cloning of murine CDK9/PITALRE and its tissue-specific expression in development (1998)

The cdc2-family of serine/threonine kinases and their binding partners recently were implicated in developmental roles. We previously cloned a cdc2-related kinase, cdk9/PITALRE, that is able to phosphorylate the retinoblastoma protein in vitro. We describe here the cloning and the characterization of the mouse homolog of cdk9/PITALRE. The murine cDNA is 98% identical with humans and is expressed at high levels in brain and kidney tissues. The kinase activity and protein expression of cdk9/PITALRE were highest in terminally differentiated tissues such as the muscle and brain. In situ immunohistology and immunofluorescence detected cdk9/PITALRE protein not only within terminally differentiated cells such as muscle and neuronal cells, but also in proliferating cells. C2C12 and P19 cells induced to differentiate along muscle and neural lineages peaked in cdk9/PITALRE kinase activity at the end of differentiation. These results suggest that, among other roles, cdk9/PITALRE plays a role not unlike cdk5 in the differentiation of certain cell types.
Unsupervised Emitter Clustering through Deep Manifold Learning (2021)

We perform unsupervised clustering to group Radio Frequency signals according to the device that transmitted the signal. We do so by first performing supervised training on a RiftNet classifier that contains a layer that can be used as a latent vector. We then perform the unsupervised clustering on a completely different set of devices than those used for training. During unsupervised clustering, we project each signal into its latent vector, then perform clustering in a UMAP-learned reduction of that space. This approach provides understanding and a path forward on how such semi-supervised deep-learning clustering approaches might fit in a real world RF system.
Characterization of exosomes from body fluids of dairy cows (2017)

Exosomes are a specific subpopulation of extracellular vesicles that are widely released by cells of different origins with divergent functions that make their way into body fluids that can be conveniently sampled. In the current study, we isolated and evaluated exosomes from concurrently collected samples of milk, plasma, saliva, and urine from a group of 6 pregnant Holstein-Friesian dairy cows (aged 7 mo, 174 to 203 d of gestation). The cows had BCS of 3.5 to 5.25 (on a scale of 1 to 10), and the milk production for the season to the time of sampling ranged between 5,118 and 6,959 kg. The low levels of extracellular vesicles in saliva and urine (more than 86% fewer compared to the extracellular vesicles in milk and plasma) precluded further detailed evaluation since utility for diagnostics was deemed unlikely. In exosomes isolated from milk and plasma, size distribution, morphology, and the presence of exosome markers was confirmed by nanoparticle tracking analysis, electron microscopy, and Western blot. In addition, a targeted proteomic approach using the quadrupole ion trap mass spectrometer was also used in the study to screen for the exosome marker (e.g., Tumor susceptibility gene 101). Following confirmation of the presence of exosomes, the proteomic profiles of milk and plasma exosomes were evaluated using information-dependent acquisition-mediated liquid chromatography-tandem mass spectrometry (LC-MS/MS). The milk exosomes contain proteins that differed greatly from the plasma exosomes, with only 8 similar proteins harbored in both the milk and plasma exosomes. The milk and plasma exosomes were found to contain proteins (e.g., immunoglobulin J chain and α2 macroglobulin) associated with specific biological processes and molecular functions. Hence, the fluid of origin required for exosome analysis will be dependent on the specific information needed. In conclusion, isolated exosomes from milk and plasma samples collected at the same time point from the same dairy cows encapsulated different profiles of proteins associated with different biological processes and molecular functions.
Pictures of relevance: A geometric analysis of similarity measures (1987)

We want computer systems that can help us assess the similarity or relevance of existing objects (e.g., documents, functions, commands, etc.) to a statement of our current needs (e.g., the query). Towards this end, a variety of similarity measures have been proposed. However, the relationship between a measure's formula and its performance is not always obvious. A geometric analysis is advanced and its utility demonstrated through its application to six conventional information retrieval similarity measures and a seventh spreading activation measure. All seven similarity measures work with a representational scheme wherein a query and the database objects are represented as vectors of term weights. A geometric analysis characterizes each similarity measure by the nature of its iso-similarity contours in an n-space containing query and object vectors. This analysis reveals important differences among the similarity measures and suggests conditions in which these differences will affect retrieval performance. The cosine coefficient, for example, is shown to be insensitive to between-document differences in the magnitude of term weights while the inner product measure is sometimes overly affected by such differences. The context-sensitive spreading activation measure may overcome both of these limitations and deserves further study. The geometric analysis is intended to complement, and perhaps to guide, the empirical analysis of similarity measures. © 1987 John Wiley & Sons, Inc.
Mitogen-regulated Ca2+ current of T lymphocytes is activated by depletion of intracellular Ca2+ stores. (1993)

Stimulated influx of Ca2+ across the plasma membrane of T lymphocytes is an essential triggering signal for T-cell activation by antigen. Regulation of the T-cell Ca2+ conductance is not understood; conflicting evidence supports direct activation by inositol 1,4,5-trisphosphate (IP3) or by a signal generated by the depletion of intracellular Ca2+ stores. We have used the perforated-patch recording technique to compare the biophysical properties of Ca2+ currents activated by T-cell receptor stimulation and by thapsigargin, a Ca(2+)-ATPase inhibitor that depletes intracellular stores without generating IP3. Both currents are blocked by Ni2+, are inwardly rectifying, are highly Ca(2+)-selective, and exhibit voltage-independent gating with a unitary chord conductance of approximately 24 fS in isotonic Ca2+. Fluctuation analysis suggests that the underlying Ca2+ transporter is a channel rather than an iron carrier. Thus, in terms of ion permeation, gating, and unitary conductance, the Ca2+ current activated by thapsigargin is indistinguishable from the elicited by crosslinking of T-cell receptors. Moreover, the unitary Ca2+ conductance is > 100-fold smaller than that of previously described IP3-gated, Ca(2+)-permeable channels in T cells [Kuno, M. & Gardner, P. (1987) Nature (London) 326, 301-304]. These results demonstrate that mitogen-activated Ca2+ influx is controlled by the state of intracellular Ca2+ stores rather than by the direct action of IP3 on Ca2+ channels in the plasma membrane.
Optimized DNA electroporation for primary human T cell engineering (2018)

Our investigation of DNA electro-transfection for the use in human primary T cell engineering established and validated an optimized method for the construction of functional CAR-T cells.
Reduced-Complexity Training Schemes for Multiple-Antenna Broadband Transmissions (2002)

This paper addresses the problem of training sequence design for multiple-antenna transmissions over quasi-static frequency-selective channels. As performance metric for channel estimation, mean square error is adopted. To achieve the minimum mean square error, the training sequences transmitted from the multiple antennas must have impulse-like auto-correlation and zero cross-correlation. We reduce the problem of designing multiple training sequences to the much easier and well-understood problem of designing a single training sequence with impulse-like auto-correlation. To this end, we propose to encode the training sequences with a space-time code, that may be the same or different from the space-time code that encodes the information symbols. Designing one instead of multiple training sequences reduces the search space significantly and simplifies the construction of optimal or suboptimal training sequences.
Multiphoton intrapulse interference IV Ultrashort laser pulse spectral phase characterization and compensation (2004)

We introduce a noninterferometric single beam method to characterize and compensate the spectral phase of ultrashort femtosecond pulses accurately. The method uses a pulse shaper that scans calibrated phase functions to determine the unknown spectral phase of a pulse. The pulse shaper can then be used to synthesize arbitrary phase femtosecond pulses or it can introduce a compensating spectral phase to obtain transform-limited pulses. This method is ideally suited for the generation of tailored spectral phase functions required for coherent control experiments.
Complete subtyping of the HLA‐A locus by sequence‐specific amplification followed by direct sequencing or single‐strand conformation polymorphism analysis (1995)

A variety of reasons related to the HLA class I system has complicated the application of molecular approaches to HLA class I typing. Here we present a PCR-based HLA-A typing strategy considering the sequence variations of the two most polymorphic exons which allows complete subtyping of the HLA-A locus. The method is based on a sequence-specific amplification identifying the serologically defined HLA-A specificities. The PCR products generated by these group-specific primers bear the sequence information necessary for a postamplification specificity step. The primer pairs are located within one exon, either exon 2 or exon 3, which avoids amplification of polymorphic intron sequences allowing subsequent single-strand conformation polymorphism analysis and facilitating direct sequencing. Using this method we investigated 48 cell lines and 153 clinical samples. 23 PCR reactions are performed per individual for the assignment of the serological specificities A1-A80. The reproducibility was 100% in all cell lines and 85 clinical samples typed on two separate occasions. With the exception of 13 out of 231 possible serological combinations all homozygous and heterozygous combinations of A1-A80 can be distinguished by specific amplification patterns. Comparing the PCR based typing results with those of serology in 12% a discrepancy was found. Solid-phase sequencing or SSCP analysis of the group-specific PCR fragments allowed complete subtyping of the HLA-A locus. This strategy can identify all 48 HLA-A alleles based on the sequence variations of the 2nd and 3rd exon. 1128 homozygous and heterozygous allele combinations are possible for the HLA-A locus. Only 4 out of these 1128 allele combinations remained unresolved.
TrueNorth: Design and Tool Flow of a 65 mW 1 Million Neuron Programmable Neurosynaptic Chip (2015)

The new era of cognitive computing brings forth the grand challenge of developing systems capable of processing massive amounts of noisy multisensory data. This type of intelligent computing poses a set of constraints, including real-time operation, low-power consumption and scalability, which require a radical departure from conventional system design. Brain-inspired architectures offer tremendous promise in this area. To this end, we developed TrueNorth, a 65 mW real-time neurosynaptic processor that implements a non-von Neumann, low-power, highly-parallel, scalable, and defect-tolerant architecture. With 4096 neurosynaptic cores, the TrueNorth chip contains 1 million digital neurons and 256 million synapses tightly interconnected by an event-driven routing infrastructure. The fully digital 5.4 billion transistor implementation leverages existing CMOS scaling trends, while ensuring one-to-one correspondence between hardware and software. With such aggressive design metrics and the TrueNorth architecture breaking path with prevailing architectures, it is clear that conventional computer-aided design (CAD) tools could not be used for the design. As a result, we developed a novel design methodology that includes mixed asynchronous-synchronous circuits and a complete tool flow for building an event-driven, low-power neurosynaptic chip. The TrueNorth chip is fully configurable in terms of connectivity and neural parameters to allow custom configurations for a wide range of cognitive and sensory perception applications. To reduce the system's communication energy, we have adapted existing application-agnostic very large-scale integration CAD placement tools for mapping logical neural networks to the physical neurosynaptic core locations on the TrueNorth chips. With that, we have successfully demonstrated the use of TrueNorth-based systems in multiple applications, including visual object recognition, with higher performance and orders of magnitude lower power consumption than the same algorithms run on von Neumann architectures. The TrueNorth chip and its tool flow serve as building blocks for future cognitive systems, and give designers an opportunity to develop novel brain-inspired architectures and systems based on the knowledge obtained from this paper.
SYNTHESIS AND USE OF SYNTHETIC OLIGONUCLEOTIDES (1984)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Expression of a heterodimeric Fab antibody protein in one cloning step. (1992)

A new method is presented for creating antibody expression libraries in Escherichia coli. Rather than perform two cloning steps to express the heavy and light chains of the antigen binding domain, we have used a fusion-PCR method to link the coding regions for heavy and light chain sequences in a single DNA molecule prior to vector ligation. This greatly simplifies the construction of antibody expression clones.
Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state (2019)

Eradicating triple-negative breast cancer (TNBC) resistant to neoadjuvant chemotherapy (NACT) is a critical unmet clinical need. In this study, patient-derived xenograft (PDX) models of treatment-naïve TNBC and serial biopsies from TNBC patients undergoing NACT were used to elucidate mechanisms of chemoresistance in the neoadjuvant setting. Barcode-mediated clonal tracking and genomic sequencing of PDX tumors revealed that residual tumors remaining after treatment with standard frontline chemotherapies, doxorubicin (Adriamycin) combined with cyclophosphamide (AC), maintained the subclonal architecture of untreated tumors, yet their transcriptomes, proteomes, and histologic features were distinct from those of untreated tumors. Once treatment was halted, residual tumors gave rise to AC-sensitive tumors with similar transcriptomes, proteomes, and histological features to those of untreated tumors. Together, these results demonstrated that tumors can adopt a reversible drug-tolerant state that does not involve clonal selection as an AC resistance mechanism. Serial biopsies obtained from patients with TNBC undergoing NACT revealed similar histologic changes and maintenance of stable subclonal architecture, demonstrating that AC-treated PDXs capture molecular features characteristic of human TNBC chemoresistance. Last, pharmacologic inhibition of oxidative phosphorylation using an inhibitor currently in phase 1 clinical development delayed residual tumor regrowth. Thus, AC resistance in treatment-naïve TNBC can be mediated by nonselective mechanisms that confer a reversible chemotherapy-tolerant state with targetable vulnerabilities.
Baroreflex control of sympathetic activity in experimental hypertension (1998)

The arterial baroreceptor reflex system is one of the most powerful and rapidly acting mechanisms for controlling arterial pressure. The purpose of the present review is to discuss data relating sympathetic activity to the baroreflex control of arterial pressure in two different experimental models: neurogenic hypertension by sinoaortic denervation (SAD) and high-renin hypertension by total aortic ligation between the renal arteries in the rat. SAD depresses baroreflex regulation of renal sympathetic activity in both the acute and chronic phases. However, increased sympathetic activity (100%) was found only in the acute phase of sinoaortic denervation. In the chronic phase of SAD average discharge normalized but the pattern of discharges was different from that found in controls. High-renin hypertensive rats showed overactivity of the renin angiotensin system and a great depression of the baroreflexes, comparable to the depression observed in chronic sinoaortic denervated rats. However, there were no differences in the average tonic sympathetic activity or changes in the pattern of discharges in high-renin rats. We suggest that the difference in the pattern of discharges may contribute to the increase in arterial pressure lability observed in chronic sinoaortic denervated rats.
The JAK2 V617F activating tyrosine kinase mutation is an infrequent event in both “atypical” myeloproliferative disorders and myelodysplastic syndromes (2005)

A somatic mutation in the JH2 autoinhibitory domain of the Janus kinase 2 (JAK2) tyrosine kinase was recently described in polycythemia vera, essential thrombocythemia, and myelofibrosis with myeloid metaplasia. The prevalence of this mutation in either "atypical" myeloproliferative disorders (MPDs) or the myelodysplastic syndromes (MDSs) is unknown. Bone marrow-derived genomic DNA from 245 patients--119 with chronic myelomonocytic leukemia (CMML), 101 with MDS, 11 with hypereosinophilic syndrome (HES), 8 with systemic mastocytosis (SM), and 6 with chronic neutrophilic leukemia (CNL)--was screened for the JAK2 V617F mutation. A mutant allele was detected in 11 patients: 3 with CMML (3%), 5 with MDS (5%), 2 with SM, and 1 with CNL. Interestingly, one of the patients with SM and the patient with CNL with JAK2 V617F had a history of lymphoma, and this patient with SM also had associated myelofibrosis and CMML. The current observation strengthens the specific association between JAK2 V617F and classic MPD, but also suggests an infrequent occurrence in other myeloid disorders.
The national cancer data base report on breast cancer (1994)

These data suggest a plateau in the use of mammographic screening.
Effect of corrosion products (neodymium iron boron) on oral fibroblast proliferation (1995)

The biological effects of the corrosion products of neodymium iron boron (Nd2Fe14B) magnets are largely unknown. The aim of this study was to identify the types of corrosion product and to evaluate the effect of the corrosion products (CP) of Nd2Fe14B magnets on the proliferation of human oral mucosal fibroblasts. Uncoated Nd2Fe14B magnets were stored in saline at 37 degrees C for 6 months and the corrosion products collected. 100 microL of a cell suspension (human oral mucosal fibroblasts [14 x 10(4) cells/mL]) was aliquoted into 72 wells of a 96-well plate, the remaining plates receiving culture medium only. After 12 h incubation at 37 degrees C, each well then received 100 microL of either (A) culture medium, (B) 100% CP, (C) 50% CP, or (D) 0% CP. The plates were reincubated at 37 degrees C for a further 48, 96, or 144 h. Fibroblast proliferation was assessed using the methylene blue uptake/elution technique. The compounds in the corrosion product were examined using quantitative X-ray analysis. Statistical analysis (ANOVA, Bonferroni's test 0.05, SAS v 6.04), showed that at each time point, the cell numbers in groups B, C, and D were significantly lower than group A. Within groups B, C, and D no significant differences were found, despite the suggestion of a dose response effect. Fibroblast proliferation in the presence of corrosion products was significantly lower than with culture medium. Fibroblast proliferation did occur in the presence of 0, 50, and 100% CP. The actual corrosion products appeared to be salts of iron but 3.2% (+/- 0.6) of neodymium chloride (NdCl3) was found.
LRRK2 in Parkinson’s disease: genetic and clinical studies from patients (2009)

Mutations in leucine-rich repeat kinase 2 (LRRK2) (PARK8) are associated with both familial and sporadic forms of Parkinson's disease. Most studies have shown that LRRK2 mutations may explain between 5% and 13% of familial and 1-5% of sporadic Parkinson's disease. Importantly, a common recurrent mutation (G2019S) located in the kinase domain has been reported across most ethnic populations, with the highest prevalence among Ashkenazi Jews and North African Arabs. A recent worldwide meta-analysis pooling data from 24 populations reported a higher occurrence of G2019S in southern than in northern European countries and the penetrance is estimated to be approximately 75% at the age of 79 years. The R1441 'hotspot' amino acid codon residue (G/H/C) in the Ras of complex proteins domain is the second most common site of pathogenic LRRK2 substitutions after G2019S, with most carriers developing symptoms by the age of 75 years. Two polymorphic variants found almost exclusively among Asians (G2385R and R1628P) have been shown to increase the Parkinson's disease risk by approximately two-fold. The mutational event associated with R1628P is more recent, occurring approximately 2500 years ago, compared to estimates of 4000 years for G2385R carriers. LRRK2 mutation carriers generally simulate late onset Parkinson's disease and present with the usual typical clinical features. Genetic testing for G2019S in sporadic late-onset Parkinson's disease can be considered in some situations and may be useful in populations with high carrier status. The identification of asymptomatic mutation and risk variant carriers provides a unique opportunity for recruiting these subjects in potential neuroprotective trials and longitudinal studies to identify biomarkers of neurodegeneration.