gebhart/patrepeval huggingface dataset:
Clinical Stabilization and Effective B-Lymphocyte Depletion in the Cerebrospinal Fluid and Peripheral Blood of a Patient With Fulminant Relapsing-Remitting Multiple Sclerosis (2005)

Our data demonstrate beneficial clinical effects of rituximab in relapsing-remitting MS, mediated through modulation of humoral systemic and central nervous system intrinsic immune responses. Clinical trials should determine optimal therapeutic strategies for patients with relapsing-remitting MS.
Cytokine Transgene Expression and Promoter Usage in Primary CD34 + Cells Using Particle-Mediated Gene Delivery (1998)

Induction or short-term transgenic expression of specific cytokines, growth factors, or other candidate therapeutic genes in hematopoietic progenitor or stem cells is potentially applicable to gene therapy for cancer. In this study, we explored the application of a gene gun technique, as an alternative to viral vectors, for ex vivo gene transfer into and transient gene expression in highly enriched CD34+ cells derived from human umbilical cord blood. Twenty-four hours posttransfection, 32.6 to 1500 pg/l x 10(6) CD34+ cells of transient gene expression was routinely obtained for specific cytokine and reporter genes. Transgene expression at the single-cell level was revealed by X-Gal staining of lacZ cDNA-transfected CD34+ cells. Expression of four candidate therapeutic genes, namely human granulocyte-macrophage colony-stimulating factor, tumor necrosis factor alpha, interleukin 2, and interferon gamma, was detectable for 4 to 7 days in CD34+ cells. A human elongation factor 1alpha promoter/intron 1 transcription unit was identified as a strong cellular promoter for CD34+ cells, exhibiting strength similar to that of the commonly employed cytomegalovirus immediate-early promoter. These results suggest that the nonviral, gene gun technique offers an efficient alternative approach for transient transgenic studies of hematopoietic cells and may provide new possibilities for certain cancer gene therapy strategies using CD34+ cells.
The pressures in the episcleral veins, Schlemm's canal and the trabecular meshwork in monkeys: Effects of changes in intraocular pressure (1989)

The pressures in the episcleral veins, Schlemm's canal and the trabecular meshwork were studied with a micropuncture technique using cannulas with tip diameters of less than 5 microns. The pressure in Schlemm's canal, Psc, was 14.3 +/- 1.0 cmH2O at spontaneous intraocular pressure, IOP, 19.2 +/- 0.9 cmH2O. The outflow pressure from the anterior chamber to Schlemm's canal was 4.9 +/- 0.7 cmH2O. The relationship between pressures was IOP = 0.73 Psc + 8.7. When the intraocular pressure was increased stepwise from the spontaneous level to 30 cmH2O there was an increase in pressure in Schlemm's canal of 1.7 +/- 0.6 cmH2O, (P less than 0.05). The total outflow resistance and the resistance between the anterior chamber and Schlemm's canal were 3.27 +/- 0.43 and 2.92 +/- 0.50 cmH2O min microliter-1 respectively for the intraocular pressure interval between the spontaneous pressure and a level 4-11 cmH2O higher. In the intraocular pressure range from 20 to 30 cmH2O the corresponding figures were 2.89 +/- 0.45 and 2.69 +/- 0.42 cmH2O min microliter-1 and for the pressure range 25-35 cmH2O, 2.48 +/- 0.58 and 2.31 +/- 0.59 cmH2O min microliter-1. The difference between the total outflow resistance and that between the anterior chamber and Schlemm's canal was about 10% of the total at intraocular pressures below 35 cmH2O. Stepwise increments in IOP increased the trabecular meshwork pressure by 0.88 cmH2O for each cmH2O increase in IOP in the interval of 30-50 cmH2O. The total outflow resistance and the resistance between the anterior chamber and the tip of the microcannula was 3.91 +/- 1.53 and 1.94 +/- 0.99 cmH2O min microliter-1 respectively for the intraocular pressure interval between the spontaneous pressure and 30 cmH2O. In the interval between 30 and 45 cmH2O the corresponding figures were 2.16 +/- 0.66 and 0.20 +/- 0.13 cmH2O min microliter-1. The episcleral venous pressure at the spontaneous intraocular pressure was 14.1 +/- 1.0 cmH2O in seven animals with minimal trauma, and 12.3 +/- 0.8 cmH2O in animals after cannulation of Schlemm's canal. The outflow pressure from the anterior chamber to the episcleral veins was 4.4 +/- 1.2 cmH2O in animals with minimal trauma and 7.1 +/- 0.8 cmH2O after cannulation of Schlemm's canal. The relationship between pressures was IOP = 0.68EVP + 11.(ABSTRACT TRUNCATED AT 400 WORDS)
Phosphate-binding proteolipid from brush border. (1982)

A proteolipid that binds inorganic phosphate with high affinity and specificity has been extracted from rabbit kidney brush-border membranes. This proteolipid has been partially purified by chromatography on LH-20. The molecular weight of the proteolipid is approximately 3000 as determined by urea-sodium dodecyl sulfate gel electrophoresis. This proteolipid can bind and transport phosphate into an organic phase. The K0.5 for phosphate binding is 8 microM with a Hill coefficient of 1.92. Arsenate inhibits phosphate binding in a competitive manner with a KI of 27.5 microM. The aminoreactive reagent 2,4-dinitrofluorobenzene inhibits phosphate binding to the proteolipid. Similarly, 2,4-dinitrofluorobenzene inhibited Na+-driven Pi uptake in renal brush-border membrane vesicles. In contrast to the mitochondrial phosphate binder, this proteolipid is not inhibited by sulfhydryl reagents. We suggest that this molecular species is a likely candidate for involvement in phosphate uptake in the renal tubule.
A Low-Power High-Performance Digital Circuit for-Deep Submicron Technologies (2005)

This paper presents a novel digital circuit design methodology that can support high-performance and low-power applications. In this method, reusing past internal voltages, signals are charged to Vdd/2 during the pre-charge cycle, so that the voltage of a signal is changed by just Vdd/2 during the evaluation cycle, resulting in a significant reduction in power consumption and propagation delay. The simulation results performed in 0.18/spl mu/m CMOS technology, demonstrate that the new circuit has three times improvement in terms of propagation delay in comparison to the equivalent domino dynamic logics. More importantly, its power consumption is 2.4 times less than that of the domino logics counterpart.
c-Met Ectodomain Shedding Rate Correlates with Malignant Potential (2006)

For a variety of human cancers, c-Met ectodomain shedding may provide a reliable and practical indicator of malignant potential and overall tumor burden.
The DNA-Binding Properties of the Major Regulatory Protein α4 of Herpes Simplex Viruses (1988)

The transition from the expression of alpha, the first set of five herpes simplex virus genes expressed after infection, to beta and gamma genes, expressed later in infection, requires the participation of infected cell protein 4 (alpha 4), the major viral regulatory protein. The alpha 4 protein is present in complexes formed by proteins extracted from infected cells and viral DNA fragments derived from promoter domains. This report shows that the alpha 4 protein forms specific complexes with DNA fragments derived from 5' transcribed noncoding domains of late (gamma 2) genes whose expression requires viral DNA synthesis as well as functional alpha 4 protein. Some of the DNA fragments to which alpha 4 binds do not contain homologs of the previously reported DNA binding site consensus sequence, suggesting that alpha 4 may recognize and interact with more than one type of DNA binding site. The alpha 4 proteins can bind to DNA directly. A posttranslationally modified form of the alpha 4 protein designated alpha 4c differs from the alpha 4a and alpha 4b forms with respect to its affinity for DNA fragments differing in the nucleotide sequences of the binding sites.
Involvement of nuclear factor kB in the regulation of cyclooxygenase‐2 expression by interleukin‐1 in rheumatoid synoviocytes (1997)

These data demonstrate that signaling via the NF-kappa B pathway is involved in regulation of COX-2 expression induced by IL-1 beta in RA synoviocytes.
Histological interaction of cultured endothelial cells and endovascular embolic materials coated with extracellular matrix (1997)

This study was undertaken to evaluate the histological reaction of cultured endothelial cells to endovascular embolic materials in vitro. Endothelial cells were isolated and cultured from a canine carotid artery. Embolic materials (platinum microcoils, polyvinyl alcohol particles, silicon balloons, or silk threads), either in their normal state or after having been coated with type 1 collagen, fibronectin, or laminin, were placed on endothelial cells and cocultured for 6, 12, and 24 hours and 2, 3, 7, 14, and 21 days. The cocultures were investigated histologically using a scanning electron microscope. Endothelial cells were not found on any uncoated embolic materials, even at 21 days. On the materials coated with fibronectin or laminin, endothelial cells began to proliferate in 7 days, covering the materials extensively in 14 days. On the other hand, endothelial cells began to proliferate on the collagen-coated materials in 3 days, covering them extensively in 7 days and reaching confluence with a cobblestone pattern in 21 days. The densities of endothelial cells on collagen-coated materials were much higher than those observed on the materials coated with other extracellular matrices. Future advantages of the clinical use of collagen-coated embolic materials in interventional treatment are discussed.
Vertical ridge augmentation around dental implants using a membrane technique and autogenous bone or allografts in humans. (1998)

This study investigated the effect on vertical bone regeneration of the addition of demineralized freeze-dried bone allograft or autogenous bone chips to a membrane technique. Twenty partially edentulous patients with vertical jawbone deficiencies were selected for this study. The patients were divided into two groups of 10 individuals. The 10 patients of Group A received 26 Brånemark implants in 10 surgical sites. The 10 patients of Group B received 32 implants in 12 surgical sites. Fifty-two out of 58 implants (22 in Group A and 30 in Group B) extended 1.5 to 7.5 mm superior to the bone crest. Titanium-reinforced expanded polytetrafluoroethylene membranes were used to cover the implants and, before complete membrane fixation, demineralized freeze-dried bone allograft particles were condensed under the membrane in Group A, and autogenous bone chips were used in Group B. At the reentry after 7 to 11 months the membranes were removed and a small biopsy was collected from 11 sites comprehending the miniscrews. The clinical measurements from Group A demonstrated a mean vertical bone gain of 3.1 mm (SD = 0.9 mm, range 1 to 5 mm) with a mean percentage of bone gain of 124% (SD = 46.6%). The measurements from Group B showed a mean vertical bone gain of 5.02 mm (SD = 2.3 mm, range 1 to 8.5 mm) with a mean percentage of bone gain of 95% (SD = 26.8%). Histomorphometric analysis of the present study clearly demonstrated a direct correlation between the density of the pre-existing bone and the density of the regenerated bone. The mean percentage of new bone-titanium contact was from 39.1% to 63.2%, depending on the quality of the pre-existing bone. Both the clinical and histologic results indicate a beneficial effect of the addition of demineralized freeze-dried bone allograft or autogenous bone particles to vertical ridge augmentation procedures in humans.
Gradient micropattern immobilization of heparin and its interaction with cells (2001)

Heparin was immobilized on a polystyrene plate in a graded micropattern by photolithography. The micropattern was confirmed by staining with brilliant green. In the presence of basic fibroblast growth factor (bFGF), the growth of NIH3T3 cells was enhanced only in the heparin-immobilized regions. This result indicated that gradient-micropattern-immobilized heparin activated bFGF for cell growth. In addition, the growth of cells was found to be affected by the surface density of immobilized heparin. The surface density was regulated by a gap length of 2 microm-width stripes immobilized with heparin. Although a high density (a region having short gap length) of immobilized heparin suppressed the cell growth in the absence of bFGF, it enhanced cell growth in the presence of bFGF. The dependence of cell function on the density of immobilized heparin was visualized by gradient-micropattern-immobilization.
Identification of transmembrane proteins as potential prognostic markers and therapeutic targets in breast cancer by a screen for signal sequence encoding transcripts (2006)

This study demonstrates, through a combination of stringent screening methods and thorough validation, that it is possible to identify transmembrane proteins preferentially expressed in primary breast tumour cells. mRNA was extracted from tumour cells isolated from invasive breast cancers and it was then subtracted against normal breast tissue mRNA prior to the generation of a signal sequence-trap library. Screening of the library identified 31 positive clones encoding 12 cell-surface and 12 secreted proteins. The expression of a subset of transmembrane genes was then interrogated using a high-throughput method (tissue microarray) coupled with cutting-edge in situ techniques in a large cohort of patients who had undergone uniform adjuvant chemotherapy. Expression of CD98 heavy chain (CD98HC) and low-level expression of the insulin-like growth factor 2 receptor/mannose-6-phosphate receptor (IGF2R/M6PR) correlated with poor patient prognosis in the whole cohort. Expression of bradykinin receptor B1 (BDKRB1) and testis enhanced gene transcript (TEGT) correlated with good prognosis in woman with oestrogen receptor (ER)-negative breast tumours. These results indicate that this combined approach of isolating primary tumour cells, generating a library to specifically isolate signal-sequence-containing transcripts, and in situ hybridization on tissue microarrays successfully identified novel prognostic markers (BDKRB1, CD98hc, and TEGT) and potential transmembrane therapeutic targets (CD98hc) in breast cancer.
Pushing Past Barriers: A glimpse of Uganda through a medical student's eyes (2010)

sickness from the helicopter ride quickly subsided as the overwhelming crowd of local villagers greeted us. In the midst of all the excitement, a mother carrying an infant infected with Yaws (a rare disfiguring infection of the bone and cartilage) caught the corner of my eye. They, as well as others, were expecting us and I was eager to help. A part of me hoped that we, as a medical team, could live up to their expectations. Last summer, I travelled with The Summer Medical Institute Northwest Medical Missions Team to provide healthcare to the isolated villages in Papua, Indonesia. These villages are located up in the mountains and are only accessible via small airplanes and helicopters. There is no electricity, no running water and many still hunt with bows and arrows. The atmosphere truly felt like a picture taken out of the pages from National Geographic. Needless to say, they had very little access to healthcare. With our limited medical supplies, we treated a variety of patients in our clinic: cleaning and dressing wounds, providing B12/ analgesic injections, treating common and complex tropical infectious diseases. Sadly, there were patients with illnesses we could not treat. However, the most memorable patient was a man who I appropriately named the “travelling patient”. After hearing our helicopter fly over his village, he trekked barefoot for 3 days just to see us. As he arrived exhausted with his feet blistered and damaged, I wondered what motivated him to endure such a grueling journey. When asked if it was worth it, he responded with simple yes, and expressed his sincere gratitude for having someone finally care for him. This experience serves as a reminder of how honored we are to be in a profession where patients actively seek our care and help. It serves as one of my driving forces to become a better physician for my future patients. It is a humbling responsibility; one I do not intend to take lightly, and the story of the travelling patient will help me to never forget this privilege. Lessons from the Travelling Patient
Tumour‐targeting bacteria‐based cancer therapies for increased specificity and improved outcome (2017)

‘You have cancer’ – a devastating diagnosis that still strikes patients hard. Despite substantial improvements of standard therapies over the years, there is still no general cure available. Here, we review the revival of an old concept – the use of bacteria as cancer therapeutics. Bacteria‐mediated tumor therapy has great potential to evolve into a powerful tool against malignant solid tumors.
Autoimmune Thrombocytopenic Purpura in Homosexual Men (1982)

Since November 1980 we have diagnosed 11 cases of severe autoimmune thrombocytopenic purpura in homosexual men; their mean platelet count (+/- SE) was 16 000 +/- 3000/mm3. All patients have been sexually active with multiple partners and exposed to numerous viruses and drugs. During this period, we also have diagnosed 20 cases of classic autoimmune thrombocytopenic purpura in heterosexual persons, with a normal women to men ratio of 3:1. Eight of nine homosexual patients had elevated platelet IgG compared with normal values in eight of 10 homosexual control subjects having normal hemograms (p less than 0.01). All responded moderately or completely to steroids. The three patients who had splenectomy had excellent responses. Four of five patients had a decreased helper/suppressor T cell ratio compared to healthy controls (p less than 0.001). Circulating immune complexes and total gamma globulin levels were elevated and lymphocytes relatively decreased in homosexual patients compared with homosexual controls (p less than 0.05). Thus, some sexually-active homosexual men seem to have an increased incidence of an immune regulation disorder directed against platelets.
THE REMOVAL OF STRONTIUM AND CESIUM FROM SIMULATED HANFORD GROUNDWATER USING INORGANIC ION EXCHANGE MATERIALS (1998)

ABSTRACT A number of inorganic ion exchange materials that are commercially available or under development were evaluated for the removal of strontium and cesium from a simulated groundwater found in the Hanford waste storage area using a groundwater simulant spiked with either 89Sr or 137 Cs. The most promising materials for strontium were found to be a sodium titanosilicate from Texas A&M University closely followed by two titanium silicate pharmacosiderites obtained from AlliedSignal. The most promising materials for the selective removal of cesium from the simulant was again the sodium titanosilicate followed by an alumina-pillared montmorillonite clay obtained from Laporte Industries Ltd. The ion exchange kinetics were shown to be very rapid for both the titanosilicate and the pharmacosiderite, whilst the alumina-pillared montmorillonite had slower kinetics more comparable to those of the zeolite AW500.
Maturation and Death of Adult-Born Olfactory Bulb Granule Neurons: Role of Olfaction (2002)

Young neurons born in the subventricular zone (SVZ) of adult mice migrate to the olfactory bulb (OB) where they differentiate into granule cells (GCs) and periglomerular interneurons. Using retroviral labeling of precursors in the SVZ, we describe five stages and the timing for the maturation of newly formed GCs: (1) tangentially migrating neuroblasts (days 2-7); (2) radially migrating young neurons (days 5-7); (3) GCs with a simple unbranched dendrite that does not extend beyond the mitral cell layer (days 9-13); (4) GCs with a nonspiny branched dendrite in the external plexiform layer (days 11-22); and (5) mature GCs (days 15-30). Using [3H]thymidine, we show that the maximum number of labeled GCs is observed around day 15 after injection. Interestingly, between days 15 and 45 after birth, soon after the cells developed spines, the number of [3H]thymidine-labeled GCs declined by 50%. Using anosmic mice, we found that sensory input was critical for the survival of GCs from day 15 to 45 after labeling. However, the number and morphology of 15-d-old cells in the granule cell layer was similar in anosmic and wild-type mice. We infer that the lack of activity did not have an effect on the generation, migration, and early differentiation of granule cells. Soon after young GCs matured, and presumably became synaptically connected, their survival depended on the level of activity that they received. This selection mechanism might allow the construction of specific OB circuits based on olfactory experience and suggests possible functions of OB cell replacement.
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes (2004)

In this paper, we present the Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. FunCat has been applied for the manual annotation of prokaryotes, fungi, plants and animals. We describe how FunCat is implemented as a highly efficient and robust tool for the manual and automatic annotation of genomic sequences. Owing to its hierarchical architecture, FunCat has also proved to be useful for many subsequent downstream bioinformatic applications. This is illustrated by the analysis of large-scale experiments from various investigations in transcriptomics and proteomics, where FunCat was used to project experimental data into functional units, as 'gold standard' for functional classification methods, and also served to compare the significance of different experimental methods. Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception.
Combining Tiled and Textual Views of Code (2014)

Jigsaw puzzle programming environments manipulate programs primarily by drag-and-drop. Generally these environments are based on their own special-purpose languages, meaning students must move on to another language as their programs grow. Tiled Grace is a tile-based editor for Grace, an educational programming language with a conventional textual syntax. Using Tiled Grace, programmers can move seamlessly between visualising their programs as tiles or source code, editing their programs via tiles or text, and continue on to traditional textual environments, all within the same programming language. We conducted a user experiment with Tiled Grace, and present the results of that experiment showing that users find dual views helpful.
Liposome-anchored local delivery of immunomodulatory agents for tumor therapy (2012)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.
Signal processing in CMOS image sensors (2002)

A CMOS image sensor codenamed EYE2, developed on a standard Intel CMOS process and designed into the Intel 971 Camera Kit, is described. EYE2 converted incident visual images into 10-bit digital data streams for still and video imaging applications. The analog signal processing that is essential to achieving the very high SNR desired is detailed. A fully differential architecture was implemented in order to achieve a desired SNR of 60 dB with known techniques for the minimization of signal degradation. The novel techniques implemented helped to speed up the analog signal path and reduced power consumption in the chip.