gebhart/patrepeval huggingface dataset:
Development of spinal neurons and tracts in the zebrafish embryo (1990)

We have analyzed pathfinding by growth cones in the spinal cord of the early zebrafish embryo, because it is an extremely simple system. At 18-20 hours of development the spinal cord contains approximately 18 lateral and presumably post-mitotic cell bodies per hemisegment. Of these 8-11 have projected growth cones by 18 hr of development and fall into five classes of neurons (Bernhardt et al., J. Comp. Neurol, preceding paper), including a set of mechanosensory (RB) neurons, three classes of interneurons (DoLA, ascending commissural, and VeLD), and previously characterized primary motor neurons (Eisen et al., '86: Nature 320:269-271). Of these five classes we analyzed pathfinding by the RB, DoLA, early ascending commissural, and VeLD neurons. These neurons are distinguishable at the earliest stages of axonogenesis based on the location of their somata and the number and initial directionality of their growth cones. In each case they follow stereotyped, cell-specific pathways to reach their termination sites. Up through larval stages exuberant axons have not been observed. The longitudinal axons of each neuronal class form bundles in the early cord. This apparently occurs because growth cones extend in close association with the longitudinal axons of the same neuronal class. At later stages spatially discrete commissural tracts are found in the cord suggesting that commissural growth cones may follow earlier commissural axons as well.
Sequencing of cDNA from 50 unrelated patients reveals that mutations in the triple-helical domain of type III procollagen are an infrequent cause of aortic aneurysms. (1993)

Detailed DNA sequencing of the triple-helical domain of type III procollagen was carried out on cDNA prepared from 54 patients with aortic aneurysms. The 43 male and 11 female patients originated from 50 different families and five different nationalities. 43 patients had at least one additional blood relative who had aneurysms. Five overlapping asymmetric PCR products, covering all the coding sequences of the triple-helical domain of type III procollagen, were sequenced with 28 specific sequencing primers. Analysis of the sequencing gels revealed only two nucleotide changes that altered the structure of the protein. One was a substitution of threonine for proline at amino acid position 501 and its functional importance was not clearly established. The other was a substitution of arginine for an obligatory glycine at amino acid position 136. In 40 of the 54 patients, detection of a polymorphism in the mRNA established that both alleles were expressed. The results indicate that mutations in type III procollagen are the cause of only about 2% of aortic aneurysms.
Expression of alpha-thymosins in human tissues in normal and abnormal growth. (1993)

Radioimmunoassays specific for the N and C termini of human prothymosin alpha and the N terminus of human parathymosin alpha were employed for the measurement of the levels of alpha-thymosins in human thymus, spleen, and liver during normal growth and intestine and breast in malignant growth. A differential expression of the two alpha-thymosins was observed in thymus (prothymosin alpha-rich) and liver (parathymosin alpha-rich). A decline in the levels of both alpha-thymosins was found with age, with prothymosin alpha in thymus showing the sharpest change (15- to 30-fold). The levels of both alpha-thymosins were higher in malignant tissues as compared with healthy ones. In breast cancer, in particular, the mean increase for prothymosin alpha and parathymosin alpha was 17.9- and 11.5-fold, respectively. The major crossreactive material was characterized in all cases as intact prothymosin alpha and parathymosin alpha. These results suggest an in vivo relationship of the expression of alpha-thymosins with the human tissue cell proliferation activity.
Lipodystrophy: metabolic insights from a rare disorder (2010)

Obesity, insulin resistance and their attendant complications are among the leading causes of morbidity and premature mortality today, yet we are only in the early stages of understanding the molecular pathogenesis of these aberrant phenotypes. A powerful approach has been the study of rare patients with monogenic syndromes that manifest as extreme phenotypes. For example, there are striking similarities between the biochemical and clinical profiles of individuals with excess fat (obesity) and those with an abnormal paucity of fat (lipodystrophy), including severe insulin resistance, dyslipidaemia, hepatic steatosis and features of hyperandrogenism. Rare lipodystrophy patients therefore provide a tractable genetically defined model for the study of a prevalent human disease phenotype. Indeed, as we review herein, detailed study of these syndromes is beginning to yield valuable insights into the molecular genetics underlying different forms of lipodystrophy, the essential components of normal adipose tissue development and the mechanisms by which disturbances in adipose tissue function can lead to almost all the features of the metabolic syndrome.
Immune System Effects of Echinacea, Ginseng, and Astragalus: A Review (2003)

Traditional herbal medicine provides several remedies for strengthening the body's resistance to illness through effects on immune system components. This review article examines 3 popular herbal immune stimulants that are often of interest to cancer patients. Echinacea, a native of North America, is widely used to prevent, or provide early treatment for, colds. Preclinical studies lend biological plausibility to the idea that echinacea works through immune mechanisms. Numerous clinical trials have been carried out on echinacea preparations: it appears that the extracts shorten the duration and severity of colds and other upper respiratory infections (URIs) when given as soon as symptoms become evident. However, trials of long-term use of echinacea as a preventive have not shown positive results. Ginseng has been studied in some depth as an antifatigue agent, but studies of immune mechanisms have not proceeded so far. Preclinical evidence shows some immune-stimulating activity. There have been several clinical trials in a variety of different diseases. Astragalus is the least-studied agent. There are some preclinical trials that show intriguing immune activity. The herbs discussed appear to have satisfactory safety profiles. Cancer patients may wish to use these botanicals to inhibit tumor growth or to boost resistance to infections. However, passive immunotherapy with herbs, with no mechanism to expose tumor antigens, is unlikely to be effective in inhibiting tumor growth. Although the margin of safety for these herbs is large, more research is needed to demonstrate the clear value of using herbs to improve resistance to infections.
Attribute-based people search in surveillance environments (2009)

We propose a novel framework for searching for people in surveillance environments. Rather than relying on face recognition technology, which is known to be sensitive to typical surveillance conditions such as lighting changes, face pose variation, and low-resolution imagery, we approach the problem in a different way: we search for people based on a parsing of human parts and their attributes, including facial hair, eyewear, clothing color, etc. These attributes can be extracted using detectors learned from large amounts of training data. A complete system that implements our framework is presented. At the interface, the user can specify a set of personal characteristics, and the system then retrieves events that match the provided description. For example, a possible query is ¿show me the bald people who entered a given building last Saturday wearing a red shirt and sunglasses.¿ This capability is useful in several applications, such as finding suspects or missing people. To evaluate the performance of our approach, we present extensive experiments on a set of images collected from the Internet, on infrared imagery, and on two-and-a-half months of video from a real surveillance environment. We are not aware of any similar surveillance system capable of automatically finding people in video based on their fine-grained body parts and attributes.
FLoc : Dependable Link Access for Legitimate Traffic in Flooding Attacks (2010)

Malware-contaminated hosts organized as a “bot network” can target and flood network links (e.g., routers). Yet, none of the countermeasures to link flooding proposed to date have provided dependable link access (i.e., bandwidth guarantees) for legitimate traffic during such attacks. In this paper, we present a router subsystem called FLoc (Flow Localization) that confines attack effects and provides differential bandwidth guarantees at a congested link: (1) packet flows of uncontaminated domains (i.e., Autonomous Systems) receive better bandwidth guarantees than packet flows of contaminated ones, and (2) legitimate flows of contaminated domains are guaranteed substantially higher bandwidth than attack flows. FLoc employs new preferential packet-drop and traffic-aggregation policies that limit “collateral damage” and protect legitimate flows from a wide variety of flooding attacks. We present FLoc's analytical model for dependable link access, a router design based on it, and illustrate FLoc's effectiveness using simulations of different flooding strategies and comparisons with other flooding defense schemes.
Analyzing Volume Diagnosis Results with Statistical Learning for Yield Improvement (2007)

A novel statistical learning algorithm is proposed to accurately analyze volume diagnosis results. This algorithm effectively overcomes the inherent ambiguities in logic diagnosis, to produce accurate feature failure probabilities, which are critical in understanding systematic yield limiters. The results of Monte-Carlo simulation are presented, which demonstrate the feasibility and impacts of various factors on this approach. Additional experiments based on injected defects are performed, which confirm the ability of this approach to generate accurate feature failure probabilities for an industrial design using actual diagnosis results.
SPEX: A Programming Language for Software Defined Radio (2006)

High-throughput, low-power Software Defined Radio(SDR) solutions require multi-core SIMD DSP processors to meet real-time performance requirements. Given the difficulty in programming traditional DSPs, these new multi-core signal processors provide even greater challenges for programmers and compilers. In this paper, we describe SPEX, a programming language which is aimed at narrowing the semantic gap between the description of complex SDR systems and their implementations. SPEX supports three different types of programming semantics, allowing SDR solutions to be developed with a divide-and-conquer approach. For DSP algorithm kernels, SPEX is able to support DSP arithmetics and first-class vector and matrix variables with sequential language semantics. From wireless protocol channels, it is able to support sequences of data-processing computations with dataflow language semantics. And for protocol systems, it is able to support real-time deadlines and concurrent executions with synchronous language semantics. The design choices are motivated by our experience implementing W-CDMA protocol on a reprogrammable substrate. In the paper, we also briefly explain SPEX’s compilation strategies. 1
Survival in a cold climate (1992)

Early in the 1980s I anticipated that sooner or later the Regional Adolescent Service based on the Young People's Unit in Macclesfield would ultimately have to face making a strong and if possible, an unanswerable case for survival.
Prevention of Thrombocytopenia by Thrombopoietin in Myelosuppressed Rhesus Monkeys Accompanied by Prominent Erythropoietic Stimulation and Iron Depletion (1997)

The effectiveness of thrombopoietin (TPO) in alleviating thrombocytopenia was evaluated in a placebo-controlled study involving rhesus monkeys exposed to 5 Gy total-body irradiation (TBI) (300-kV x-rays) to result in 3 weeks of pancytopenia. Supraoptimal treatment with human recombinant TPO (10 μg/kg/d subcutaneously, days 1 to 21 after TBI) was highly effective in preventing thrombocytopenia, with nadirs for thrombocytes, on average, far higher than 100 × 109/L, a greatly accelerated recovery to normal values, and no need for thrombocyte transfusions. TPO appeared to act selectively in that neutrophil regeneration was not influenced but red blood cell lineage recovery was prominently stimulated, with reticulocyte regeneration being initiated 10 days earlier than in placebo-treated animals. The reticulocytosis was followed by a normoblastosis that occurred earlier and was more pronounced than in placebo-treated monkeys. The effect of TPO on the red blood cell lineage was also reflected in a less profound nadir for hemoglobin (Hb) and hematocrit values than in placebo controls. However, this effect was not followed by a rapid recovery to normal values, due to development of a microcytic hypochromic anemia. Iron depletion was demonstrated by measurements of total serum iron and total iron-binding capacity (TIBC) and could be prevented by prophylactic intramuscular (IM) iron before TBI or corrected by IM iron after TPO treatment. Rechallenging with TPO in week 8 after TBI demonstrated a homogenous thrombocyte response similar in magnitude to the initial response, but a greatly diminished reticulocyte response. This demonstrated that the erythropoietic response to TPO administration depends on the hemopoietic state of the animal and may reflect multiple TPO target cells. It is postulated that the extremely rapid erythropoiesis due to TPO treatment in the initial regeneration phase following myelosuppression results in iron depletion by a mechanism similar to that seen following erythropoietin treatment in patients with end-stage renal failure. It is concluded that protracted TPO therapy to counteract thrombocytopenic states may result in iron depletion and that the iron status should be monitored before, during, and after TPO treatment.
[Isolation of cDNA clones which are specifically transcribed in metastatic and nonmetastatic murine tumors]. (1989)

Gene cloning was used with a view to examine differences in gene expression in metastatic (CSML-100) and non-metastatic (CSML-0) cell lines. Differential screening of the cDNA libraries obtained was performed. Mts271 gene which is specifically expressed in metastatic cells was isolated.
Inhibition of ubiquitin-protein ligase (E3) by mono- and bifunctional phenylarsenoxides. Evidence for essential vicinal thiols and a proximal nucleophile. (1992)

Trivalent arsenoxides bind to vicinal thiol groups of proteins. We showed previously that the simplest trivalent arsenoxide, inorganic arsenite, inhibits ubiquitin-dependent protein degradation in rabbit reticulocyte lysate (Klemperer, N.S., and Pickart, C.M. (1989) J. Biol. Chem. 264, 19245-19242). We now show that, relative to arsenite, phenylarsenoxides are 10-165-fold more potent inhibitors of protein degradation in the same system (K0.5 for inhibition by p-aminophenylarsenoxide was 3.5-20 microM, depending on the substrate). In the ubiquitin-dependent proteolytic pathway, covalent ligation of ubiquitin to protein substrates targets the latter for degradation. In certain cases, specificity in ubiquitin-substrate conjugation depends critically upon the properties of ubiquitin-protein ligase or E3. Among other effects, p-aminophenylarsenoxide decreased the steady-state level of ubiquitinated human alpha-lactalbumin; this is a substrate which is acted upon directly by ubiquitin-protein ligase-alpha (E3-alpha). This finding suggests that phenylarsenoxides (unlike arsenite) inhibit E3. Several other lines of evidence confirm this conclusion. 1) A complex of E3-alpha and the 14-kDa ubiquitin-conjugating (E2) isozyme binds to phenylarsenoxide-Sepharose resin, with the E3 component of the complex mediating binding. 2) p-Aminophenylarsenoxide inhibited isolated E3 (K0.5 approximately 50 microM); inhibition was readily reversed by addition of dithiothreitol (which contains a competing vicinal thiol group), but not by beta-mercaptoethylamine (a monothiol). 3) A bifunctional phenylarsenoxide (bromoacetylaminophenylarsenoxide) rapidly and irreversibly inactivated E3; bromoacetyl aniline, which lacks an arsenoxide moiety, did not inhibit E3. These results suggest that E3 possesses essential vicinal thiol groups and that there is a reactive nucleophile proximal to the vicinal thiol site. The bifunctional phenylarsenoxide should be a useful tool for probing the relationship between structure and function in E3. As expected from prior results with arsenite, p-aminophenylarsenoxide was also a potent inhibitor of the turnover of ubiquitin-(human) alpha-lactalbumin conjugates.
A Fatal Case of Progressive Vaccinia — Clinical and Pathological Studies (1977)

The clinical and pathological details of an infant aged 1 year with progressive vaccinia are presented. Evidence of combined cellular and humoral deficiency was obtained in this infant during life. Despite therapy with hyperimmune gammaglobulin, N-methylisatin, B-thiosemicarbisone (methisazone), antibiotics and transfer factor, death occurred. Autopsy revealed thymic dysplasia and atrophy of lymphoid tissue within lymph nodes, spleen, tonsils and gastrointestinal tract. Recommendations regarding the management of progressive vaccinia are made.
Collapse-to-zoom (2004)

Overview visualizations for small-screen web browsers were designed to provide users with visual context and to allow them to rapidly zoom in on tiles of relevant content. Given that content in the overview is reduced, however, users are often unable to tell which tiles hold the relevant material, which can force them to adopt a time-consuming hunt-and-peck strategy. Collapse-to-zoom addresses this issue by offering an alternative exploration strategy. In addition to allowing users to zoom into relevant areas, collapse-to-zoom allows users to collapse areas deemed irrelevant, such as columns containing menus, archive material, or advertising. Collapsing content causes all remaining content to expand in size causing it to reveal more detail, which increases the user's chance of identifying relevant content. Collapse-to-zoom navigation is based on a hybrid between a marquee selection tool and a marking menu, called marquee menu. It offers four commands for collapsing content areas at different granularities and to switch to a full-size reading view of what is left of the page.
Inhibition of insulin-like growth factor-1 receptor signaling enhances growth-inhibitory and proapoptotic effects of gefitinib (Iressa) in human breast cancer cells (2005)

These results indicate that IGF-1R signaling reduces the antiproliferative effects of gefitinib in several breast cancer cell lines, and that the addition of an anti-IGF-1R strategy to gefitinib treatment may be more effective than a single-agent approach.
Comparison of frozen and RNALater solid tissue storage methods for use in RNA expression microarrays (2004)

Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue. This nontoxic preservative enables decentralized tissue collection for expression array analysis without a requirement for specialized equipment.
Brillouin amplification in phase coherent transfer of optical frequencies over 480 km fiber (2010)

We describe the use of fiber Brillouin amplification (FBA) for the coherent transmission of optical frequencies over a 480 km long optical fiber link. FBA uses the transmission fiber itself for efficient, bi-directional coherent amplification of weak signals with pump powers around 30 mW. In a test setup we measured the gain and the achievable signal-to-noise ratio (SNR) of FBA and compared it to that of the widely used uni-directional Erbium doped fiber amplifiers (EDFA) and to our recently built bi-directional EDFA. We measured also the phase noise introduced by the FBA and used a new and simple technique to stabilize the frequency of the FBA pump laser. We then transferred a stabilized laser frequency over a wide area network with a total fiber length of 480 km using only one intermediate FBA station. After compensating the noise induced by the fiber, the frequency is delivered to the user end with an uncertainty below 2 x 10(-18) and an instability sigma y(tau) = 2 x 10(-14) /(tau/s).
Microfluidic System for Automated Cell-Based Assays (2007)

Microfluidic cell culture is a promising technology for applications in the drug screening industry. Key benefits include improved biological function, higher quality cell-based data, reduced reagent consumption, and lower cost. In this work, we demonstrate how a microfluidic cell culture design was adapted to be compatible with the standard 96-well plate format. Key design features include the elimination of tubing and connectors, the ability to maintain long term continuous perfusion cell culture using a passive gravity driven pump, and direct analysis on the outlet wells of the microfluidic plate. A single microfluidic culture plate contained 8 independent flow units, each with 10(4) cells at a flow rate of 50 μl/day (6 minute residence time). The cytotoxicity of the anti-cancer drug etoposide was measured on HeLa cells cultured in this format, using a commercial lactate dehydrogenase (LDH) plate reader assay. The integration of microfluidic cell culture methods with commercial automation capabilities offers an exciting opportunity for improved cell-based screening.
Benzothiophene Selective Estrogen Receptor Modulators with Modulated Oxidative Activity and Receptor Affinity (2007)

The regulation of estrogenic and antiestrogenic effects of selective estrogen receptor modulators (SERMs) is thought to underlie their clinical use. Most SERMs are polyaromatic phenols susceptible to oxidative metabolism to quinoids, which are proposed to be genotoxic. Conversely, the redox reactivity of SERMs may contribute to antioxidant and chemopreventive mechanisms, providing a new approach to improve the therapeutic properties of SERMs. An improved synthetic strategy was developed to generate a family of benzothiophene SERMs. Using computational modeling methods and measurements of antioxidant activity and estrogen receptor (ER) ligand binding, this SERM family was shown to provide both a range of ERalpha/ERbeta selectivity from 1.2- to 67-fold and a range of redox activity. Antioxidant activity was successfully modulated by varying a substituent remote from the OH group; the source of the antioxidant capacity. An efficient synthetic procedure is reported yielding benzothiophene SERMs wherein redox activity and ER affinity are modulated.