gebhart/patrepeval huggingface dataset:
Assembly of ER-associated protein degradation in vitro: dependence on cytosol, calnexin, and ATP. (1996)

To investigate the mechanisms of ER-associated protein degradation (ERAD), this process was reconstituted in vitro. Established procedures for post-translational translocation of radiolabeled prepro-alpha factor into isolated yeast microsomes were modified to inhibit glycosylation and to include a posttranslocation "chase" incubation period to monitor degradation. Glycosylation was inhibited with a glyco-acceptor peptide to compete for core carbohydrates, or by using a radio-labeled alpha factor precursor that had been genetically engineered to eliminate all three glycosylation sites. Inhibition of glycosylation led to the production of unglycosylated pro-alpha factor (p alpha F), a processed form of the alpha factor precursor shown to be a substrate of ERAD in vivo. With this system, both glycosylated and unglycosylated forms of pro-alpha factor were stable throughout a 90-min chase incubation. However, the addition of cytosol to the chase incubation reaction induced a selective and rapid degradation of p alpha F. These results directly reflect the behavior of alpha factor precursor in vivo; i.e., p alpha F is a substrate for ERAD, while glycosylated pro-alpha factor is not. Heat inactivation and trypsin treatment of cytosol, as well as addition of ATP gamma S to the chase incubations, led to a stabilization of p alpha F. ERAD was observed in sec12 microsomes, indicating that export of p alpha F via transport vesicles was not required. Furthermore, p alpha F but not glycosylated pro-alpha factor was found in the supernatant of the chase incubation reactions, suggesting a specific transport system for this ERAD substrate. Finally, the degradation of p alpha F was inhibited when microsomes from a yeast strain containing a disrupted calnexin gene were examined. Together, these results indicate that cytosolic protein factor(s), ATP hydrolysis, and calnexin are required for ER-associated protein degradation in yeast, and suggest the cytosol as the site for degradation.
Correlation of mRNA and protein levels: Cell type-specific gene expression of cluster designation antigens in the prostate (2008)

: Agreement between these two very different methodologies has great implications for their respective use in both molecular studies and clinical trials employing molecular biomarkers.
Is keeping cool still hot? An update on hypothermia in brain injury (2004)

Hypothermia is a useful adjunct to barbiturates and mannitol to control elevated intracranial pressure. The results of trials that have tested systemic hypothermia as a neuroprotectant have been negative or equivocal, and cooling may have been induced outside the treatment window.
In vitro IgE formation by peripheral blood lymphocytes from normal individuals and patients with allergic bronchopulmonary aspergillosis. (1980)

Peripheral blood lymphocytes from five normal donors and five individuals with allergic bronchopulmonary aspergillosis (ABPA) were used for measurement of in vitro IgE formation in tissue culture preparations. IgE was measured by a sensitive radioimmunoassay using concentrated tissue culture medium (TCM) and expressed as ng IgE/ml of TCM. The results demonstrated that IgE was formed by unstimulated lymphocytes from one of five normal donors (range 1.5-2.4 ng/ml) and in two of five ABPA donors (range 2-4 ng/ml). However, when different dilutions of pokeweed mitogen were added to the tissue culture, three of five normal donors and three of five ABPA donors in remission showed enhanced IgE formation. At the time of an ABPA exacerbation in one individual, there was a definite increse in IgE synthesis up to 40 ng/ml which was suppressed by pokeweed mitogen to 17.3 ng/ml. Clear differences between normals and ABPA patients in remission are not apparent.
In vitro fermentation of carbohydrate by breast fed and formula fed infants (1997)

Unabsorbed carbohydrates are fermented by colonic bacteria to short chain fatty acids (SCFA) which are rapidly absorbed, salvaging energy and reducing stool output. There are marked differences between the faecal flora and SCFA of breast fed (BF) and formula fed (FF) infants which may be related to the higher incidence of diarrhoea in FF infants. Part of this effect may be caused by a difference in the ability of the microflora to ferment carbohydrate. To test the hypothesis that BF and FF have different fermentation capacities for simple and complex carbohydrates, in vitro cultures of faeces from healthy infants (2-10 weeks; 11 BF, 11 FF) containing glucose, lactose, raftilose (a fructo-oligosaccharide), or soybean polysaccharide were incubated anaerobically. Results were compared with those of adult faecal cultures using the same carbohydrates. Cultures of faeces from BF and FF infants produced comparable amounts of total SCFA in all cultures. These cultures produced less SCFA than those from adult faeces and produced very little SCFA from complex carbohydrate. BF cultures produced more acetic acid than FF in all cultures, whereas FF cultures produced more propionate with sugars and more butyrate with raftilose. Both groups of infants produced less butyrate than adults in all cultures. Thus it is unlikely that a lower ability to ferment carbohydrate is a major cause of increased risk of diarrhoea in FF fed infants but individual SCFA production may be important.
Using a self-organizing neural network for wafer defect inspection (2005)

Wafer defect inspection is an important process before die packaging. The defective regions are usually identified through visual judgment with the aid of a scanning electron microscope. Five to ten people visually check wafers and hand-mark their defective regions. By this means, potential misjudgment may be introduced due to human fatigue. In addition, the process can incur significant personnel costs. Self-organizing neural networks (SONN) have been proven to have the capabilities of auto-clustering. Automated wafer inspection based on a self-organizing neural network is proposed to replace the traditional electrical testing and the human inspection process. Based on real world data, experimental results show that the proposed method successfully identifies the defective regions on wafers with good performances.
Serum Th1 and Th2 cytokine balance in patients of superficial transitional cell carcinoma of bladder pre- and post-intravesical combination immunotherapy (2010)

Combination therapy with intravesical bacillus Calmette-Guerin (BCG) plus interferon-alpha2b (IFN-alpha2b) for superficial transitional cell carcinoma (TCC) seems to be immune-dependent and activation of Th1 immune response is required for clinical efficacy. The present study evaluates circulating serum cytokine profiles (Th1/Th2 cytokines IFN-gamma, IL-2 TNF-alpha, IL-4, IL-6 and IL-10) in 41 bladder cancer patients prior to transurethral resection of tumor (TURBT) (pre-therapy), and following intravesical combination immunotherapy (post-therapy) and their association with recurrence. Mean levels of IL-2 and TNF-alpha were significantly reduced while IL-4, IL-6 and IL-10 were significantly enhanced in pre-therapy samples as compared to controls. Mean levels of IFN-gamma, IL-2 and TNF-alpha were significantly increased while IL-4 and IL-10 were significantly reduced in patients after instillation of combination immunotherapy. These findings suggest that bladder cancer patients develop Th2 dominant status with deficient type 1 immune response that shows tendency to reversal following therapy.
RET Germline Mutations Identified by Exome Sequencing in a Chinese Multiple Endocrine Neoplasia Type 2A/Familial Medullary Thyroid Carcinoma Family (2011)

The results confirmed the successful clinical utility of whole exome sequencing, and our data suggested that the p.C634Y/V292M/R67H/R982C mutation of RET exhibited a more aggressive clinical phenotype than p.C634Y or p.V292M/R67H/R982C, while p.V292M/R67H/R982C presented a relatively milder pathogenicity of MTC and likely predisposed to FMTC.
Coordinated leading- and lagging-strand synthesis at the Escherichia coli DNA replication fork. I. Multiple effectors act to modulate Okazaki fragment size. (1992)

The coordinated action of many enzymatic activities is required at the DNA replication fork to ensure the error-free, efficient, and simultaneous synthesis of the leading and lagging strands of DNA. In order to define the essential protein-protein interactions and model the regulatory pathways that control Okazaki fragment synthesis, we have reconstituted the replication fork of Escherichia coli in vitro in a rolling circle-type DNA replication system. In this system, in the presence of the single-stranded DNA binding protein, the helicase/primase function on the lagging-strand template is provided by the primosome, and the synthesis of DNA strands is catalyzed by the DNA polymerase III holoenzyme. These reconstituted replication forks synthesize equivalent amounts of leading- and lagging-strand DNA, move at rates comparable to those measured in vivo (600-800 nucleotides/s at 30 degrees C), and can synthesize leading strands in the range of 150-500 kilobases in length. Using this system, we have studied the cycle of Okazaki fragment synthesis at the replication fork. This cycle is likely to have several well defined decision points, steps in the cycle where incorrect execution by the enzymatic machinery will result in an alteration in the product of the reaction, i.e. in the size of the Okazaki fragments. Since identification of these decision points should aid in the determination of which of the enzymes acting at the replication fork control the cycle, we have endeavored to identify those reaction parameters that, when varied, alter the size of the Okazaki fragments synthesized. Here we demonstrate that some enzymes, such as the DnaB helicase, remain associated continuously with the fork while others, such as the primase, must be recruited from solution each time synthesis of an Okazaki fragment is initiated. We also show that variation of the concentration of the ribonucleoside triphosphates and the deoxyribonucleoside triphosphates affects Okazaki fragment size, that the control mechanisms acting at the fork to control Okazaki fragment size are not fixed at the time the fork is assembled but can be varied during the lifetime of the fork, and that alteration in the rate of the leading-strand DNA polymerase cannot account for the effect of the deoxyribonucleoside triphosphates.
Ethanol sensitizes NF-κB activation in pancreatic acinar cells through effects on protein kinase C-ε (2006)

Although ethanol abuse is the most common cause of pancreatitis, the mechanism of alcohol's effect on the pancreas is not well understood. Previously, we demonstrated that in vitro ethanol treatment of pancreatic acinar cells augmented the CCK-8-induced activation of NF-kappaB, a key signaling system involved in the inflammatory response of pancreatitis. In the present study, we determine the role for individual PKC isoforms in the sensitizing effect of ethanol on NF-kappaB activation. Dispersed rat pancreatic acini were treated with and without ethanol and then stimulated with CCK-8; 100 nM CCK-8 caused both NF-kappaB and PKC-delta, -epsilon, and -zeta activation, whereas 0.1 nM CCK-8 did not increase PKC-epsilon, PKC-zeta, or NF-kappaB activity. CCK-8 (0.1 nM) did activate PKC-delta. PKC-epsilon activator alone did not cause NF-kappaB activation; however, together with 0.1 nM CCK-8, it caused NF-kappaB activation. Ethanol activated PKC-epsilon without affecting other PKC isoforms or NF-kappaB activity. Of note, stimulation of acini with ethanol and 0.1 nM CCK-8 resulted in the activation of PKC-delta, PKC-epsilon, and NF-kappaB. The NF-kappaB activation to 0.1 nM CCK-8 in ethanol-pretreated acini was inhibited by both PKC-delta inhibitor and PKC-epsilon inhibitor. Taken together, these results demonstrate the different modes of activation of PKC isoforms and NF-kappaB in acini stimulated with ethanol, high-dose CCK-8, and low-dose CCK-8, and furthermore suggest that activation of both PKC-epsilon and -delta is required for NF-kappaB activation. These results suggest that ethanol enhances the CCK-8-induced NF-kappaB activation at least in part through its effects on PKC-epsilon.
Organization of the resting TCR in nanoscale oligomers (2012)

Despite the low affinity of the T-cell antigen receptor (TCR) for its peptide/major histocompatibility complex (pMHC) ligand, T cells are very sensitive to their antigens. This paradox can be resolved if we consider that the TCR may be organized into pre-existing oligomers or nanoclusters. Such structures could improve antigen recognition by increasing the functional affinity (avidity) of the TCR-pMHC interaction and by allowing cooperativity between individual TCRs. Up to approximately 20 TCRs become tightly apposed in these nanoclusters, often in a linear manner, and such structures could reflect a relatively generalized phenomenon: the non-random concentration of membrane receptors in specific areas of the plasma membrane known as protein islands. The association of TCRs into nanoclusters can explain the enhanced kinetics of the pMHC-TCR interaction in two dimensional versus three dimensional systems, but also their existence calls for a revision of the TCR triggering models based on pMHC-induced TCR clustering. Interestingly, the B-cell receptor and the FcεRI have also been shown to form nanoclusters, suggesting that the formation of pre-existing receptor oligomers could be widely used in the immune system.
Heel contact as a function of substrate type and speed in primates (1995)

In this report we provide detailed data on the patterns and frequency of heel contact with terrestrial and arboreal supports in primates. These data can help resolve the question of whether African apes and humans are uniquely "plantigrade" (Gebo [1992] Am. J. Phys. Anthropol. 89:29-58; Gebo [1993a] Am. J. Phys. Anthropol. 91:382-385; Gebo [1993b] Postcranial Adaptation in Nonhuman Primates), or if plantigrady is common in other primates (Meldrum [1993] Am. J. Phys. Anthropol. 91:379-381). Using biplanar and uniplanar videotapes, we recorded the frequency and timing of heel contact for a variety of primates (32 species) walking on the ground and on simulated arboreal supports at a range of natural speeds. Our results indicate that Pongo as well as the African apes exhibit a "heel-strike" at the end of swing phase. Ateles and Hylobates make heel contact on all supports shortly after mid-foot contact, although spider monkeys do so only at slow or moderate speeds. Data available from uniplanar videotapes suggest that this pattern occurs in Alouatta and Lagothrix as well. No other New or Old World monkey or prosimian in this study made heel contact during quadrupedalism on any substrate. Thus, heel contact occurs in all apes and atelines, but only the great apes exhibit a heel-strike. We suggest that heel contact with the substrate is a by-product of an active posterior weight-shift mechanism involving highly protracted hindlimbs at touchdown. Force plate studies indicate that this mechanism is most extreme in arboreally adapted primate quadrupeds walking on arboreal supports. Although heel contact and heel-strike may have no evolutionary link, it is possible that both patterns are the result of a similar weight shift mechanism. Therefore, the regular occurrence of heel contact in a variety of arboreal primates, and the absence of a true biomechanical link between limb elongation, heel contact, and terrestriality, calls into question the claim that hominid foot posture was necessarily derived from a quadrupedal terrestrial ancestor.
Extracorporeal human whole blood in motion, as a tool to predict first-infusion reactions and mechanism-of-action of immunotherapeutics (2017)

First infusion reactions along with severe anaphylactic responses can occur as a result of systemic administration of therapeutic antibodies. The underlying mechanisms by which monoclonal antibodies induce cytokine release syndrome (CRS) can involve direct agonistic effects via the drug target, or a combination of target-engagement along with innate receptor interactions. Despite the wide variety of pathways and cells that can play a role in CRS, many currently used assays are devoid of one or more components that must be present for these responses to occur. One assay that has not been assessed for its capacity to predict CRS is the modified Chandler loop model. Herein we evaluate a plethora of commercially available monoclonal antibodies to evaluate the modified Chandler loop model's potential in CRS prediction. We demonstrate that in a 4-hour loop assay, both the superagonistic antibodies, anti-CD3 (OKT3) and anti-CD28 (ANC28.1), display a clear cytokine response with a mixed adaptive/innate cytokine source. OKT3 induce TNFα and IFN-γ release in 20 out of 23 donors tested, whereas ANC28.1 induce TNF-α, IL-2 and IFN-γ release in all donors tested (n=18-22). On the other hand, non-agonistic antibodies associated with no or low infusion reactions in the clinic, namely cetuximab and natalizumab, neither induce cytokine release nor cause false positive responses. A TGN1412-like antibody also display a clear cytokine release with an adaptive cytokine profile (IFN-γ and IL-2) and all donors (n=9) induce a distinct IL-2 response. Additionally, the value of an intact complement system in the assay is highlighted by the possibility to dissect out the mechanism-of-action of alemtuzumab and rituximab. The loop assay can either complement lymph node-like assays or stand-alone to investigate drug/blood interactions during preclinical development, or for individual safety screening prior to first-in-man clinical trial.
Unexpectedly Limited Durability of Immunity Following Acellular Pertussis Vaccination in Preadolescents in a North American Outbreak (2012)

Our data suggests that the current schedule of acellular pertussis vaccine doses is insufficient to prevent outbreaks of pertussis. We noted a markedly increased rate of disease from ages 8-12 years, proportionate to the interval since the last scheduled vaccine. Stable rates of testing ruled out selection bias. The possibility of earlier or more numerous booster doses of acellular pertussis vaccine either as part of routine immunization or for outbreak control should be entertained.
The Role of Antibody Polyspecificity and Lipid Reactivity in Binding of Broadly Neutralizing Anti-HIV-1 Envelope Human Monoclonal Antibodies 2F5 and 4E10 to Glycoprotein 41 Membrane Proximal Envelope Epitopes (2007)

Two neutralizing human mAbs, 2F5 and 4E10, that react with the HIV-1 envelope gp41 membrane proximal region are also polyspecific autoantibodies that bind to anionic phospholipids. To determine the autoantibody nature of these Abs, we have compared their reactivities with human anti-cardiolipin mAbs derived from a primary antiphospholipid syndrome patient. To define the role of lipid polyreactivity in binding of 2F5 and 4E10 mAbs to HIV-1 envelope membrane proximal epitopes, we determined the kinetics of binding of mAbs 2F5 and 4E10 to their nominal gp41 epitopes vs liposome-gp41 peptide conjugates. Both anti-HIV-1 mAbs 2F5 and 4E10 bound to cardiolipin with K(d) values similar to those of autoimmune anti-cardiolipin Abs, IS4 and IS6. Binding kinetics studies revealed that mAb 2F5 and 4E10 binding to their respective gp41 peptide-lipid conjugates could best be defined by a two-step (encounter-docking) conformational change model. In contrast, binding of 2F5 and 4E10 mAbs to linear peptide epitopes followed a simple Langmuir model. A mouse mAb, 13H11, that cross-blocks mAb 2F5 binding to the gp41 epitope did not cross-react with lipids nor did it neutralize HIV-1 viruses. Taken together, these data demonstrate the similarity of 2F5 and 4E10 mAbs to known anti-cardiolipin Abs and support the model that mAb 2F5 and 4E10 binding to HIV-1 involves both viral lipid membrane and gp41 membrane proximal epitopes.
Expression of the activation antigen CD69 predicts functionality ofin vitroexpanded peripheral blood mononuclear cells (PBMC) from healthy donors and HIV-infected patients (1998)

Gene therapy for AIDS necessitates harvest and expansion of PBMC from HIV-infected patients. We expanded PBMC from healthy blood donors and HIV-infected patients for up to 14 days using four expansion protocols: 3 days of phytohaemagglutinin (PHA) stimulation, continuous PHA stimulation, 3 days of stimulation with anti-CD3 and anti-CD28, and continuous stimulation with anti-CD3 and anti-CD28. Functionality of PBMC was evaluated prior to and after expansion using standard proliferation assay. Phenotype and lymphocyte subset activation defined by expression of CD69 and CD25 were determined using flow cytometry. PBMC from healthy donors and HIV-infected patients were readily expanded. The best expansion was obtained using stimulation for 3 days. After expansion, functionality of PBMC measured as proliferative response was partly conserved. PBMC expanded with stimulation for 3 days exhibited more preserved functionality than PBMC stimulated continuously (P < 0.03). The mean proliferative response in each of the four different expansion protocols correlated with the mean values of CD69 expression. The proliferative responses from patients and healthy donors expanded with PHA stimulation for 3 days correlated with CD69 expression on CD4 cells (r = 0.68, P < 0.01) and on CD8 cells (r = 0.59, P < 0.03). Furthermore, expression of CD69 reliably predicted which patients and donors had highly conserved functionality after in vitro expansion. Finally, PBMC expanded with PHA stimulation for 3 days were examined for apoptosis. Only a minor fraction was primed for apoptosis, and this fraction could be significantly reduced by addition of IL-2 to the culture medium (P < 0.05). In conclusion, the feasibility of expanding PBMC from HIV patients was demonstrated. Expanded PBMC had conserved functionality. Finally, after in vitro expansion, expression of the activation antigen CD69 reliably predicted functionality of PBMC.
Comparison of four approaches to automatic language identification of telephone speech (1996)

Abstruct- We have compared the performance of four approaches for automatic language identification of speech utterances: Gaussian mixture model (GMM) classification; single-language phone recognition followed by languagedependent, interpolated n-gram language modeling (PRLM); parallel PRLM, which uses multiple single-language phone recognizers, each trained in a different language; and languagedependent parallel phone recognition (PPR). These approaches, which span a wide range of training requirements and levels of recognition complexity, were evaluated with the Oregon Graduate Institute Multi-Language Telephone Speech Corpus. Systems containing phone recognizers performed better than the simpler GMM classifier. The top-performing system was parallel PRLM, which exhibited an error rate of 2% for 45-s utterances and 5% for 10-s utterances in two-language, closed-set, forcedchoice classification. The error rate for 11-language, closed-set, forced-choice classification was 11 % for 45-s utterances and 21% for 10-s utterances.
Field Emitter Equipped With a Suppressor to Control Emission Angle (2013)

We introduce a suppressor electrode into a micro-sized field emitter to control the emission angle, as an alternative to using an aperture. The suppressor electrode is fabricated between the emission tip and the extractor by using an etch-back technique. The suppressor height is determined to be 100 nm below the tip. This structure is expected to control the emission angle to be narrower when applying a low voltage at the suppressor electrode. The emission characteristics of the fabricated device closely follow the behavior of the simulated results. It is shown that the emission angle is narrowed by applying a negative voltage at the suppressor electrode.