gebhart/patrepeval huggingface dataset:
Single Trial Classification of Motor Imagination Using 6 Dry EEG Electrodes (2007)

Our study shows that a surprisingly simple and convenient method of brain activity imaging is possible, and that simple and robust analysis techniques exist which discriminate among mental states in single trials. Within 15 minutes the dry BCI device is set-up, calibrated and ready to use. Peak performance matched reported EEG BCI state of the art in one subject. The results promise a practical non-invasive BCI solution for severely paralyzed patients, without the bottleneck of setup effort and limited recording duration that hampers current EEG recording technique. The presented recording method itself, BCI not considered, could significantly widen the use of EEG for emerging applications requiring long-term brain activity and mental state monitoring.
Emerging anti-cancer molecular mechanisms of aminobisphosphonates (2006)

Bone metastases are common in patients with many types of cancer, especially breast and prostate cancer--in which the incidence is approximately 70% among patients with advanced metastatic disease. Aminobisphosphonates (NBPs) have entered clinical practice in the treatment of bone metastases from several neoplasms, including breast and prostate adenocarcinoma, as a result of their anti-resorption properties. However, evidence has accumulated on the direct anti-tumour effects of NBPs. This review describes the metabolic pathways that are putative molecular targets of NBPs and that are involved in the prenylation processes of several intracellular small GTP-binding proteins (ras family related proteins). The latter regulate the intracellular survival and proliferative pathways of tumour cells and could be the intracellular molecular targets of the NBPs responsible for the direct anti-cancer effects, even if definitive conclusions cannot be drawn at present. Different mechanisms have been reported to account for the anti-neoplastic action of NBPs, including: the induction of apoptosis; cell cycle perturbations; and anti-invasive, anti-migration and anti-angiogenic effects. Moreover, this review describes the most important clinical studies that demonstrate the activity of NBPs in preventing skeletal-related events induced by bone metastases. The main pharmacokinetic pitfalls of NBPs are described, and methods of overcoming these pitfalls through the use of liposome vehicles are proposed. Finally, the principal pre-clinical studies on the interaction between NBPs and other biological agents are also described; these studies may enable reductions in the in vivo NBP concentrations required to achieve anti-tumour activity. To date, however, the real molecular targets of NBPs are not completely known and new technological platforms are required in order to detect them and to develop new anti-cancer strategies based on the use of NBPs.
Biofilm Formation on Hydrophilic Intraocular Lens Material (2006)

The biofilm formation was less on hydrogel than on other two materials tested. Hydrogel presoaked in antibiotics exhibited a preventive effect against biofilm formation at least for 24 hr in vitro and against bacterial proliferation in the rabbit in vivo endophthalmitis model.
Color and monochrome lensless on-chip imaging of Caenorhabditis elegans over a wide field-of-view (2010)

We demonstrate color and monochrome on-chip imaging of Caenorhabditis elegans samples over a wide field-of-view using incoherent lensless in-line holography. Digital reconstruction of the recorded lensless holograms rapidly creates the C. elegans images within <1 s over a field-of-view of >24 mm2. By digitally combining the reconstructed images at three different wavelengths (red, green and blue), color images of dyed samples are also acquired. This wide field-of-view and compact on-chip imaging modality also permits straightforward integration with microfluidic systems.
Signature files (1984)

The signature-file access method for text retrieval is studied. According to this method, documents are stored sequentially in the "text file." Abstractions ("signatures") of the documents are stored in the "signature file." The latter serves as a filter on retrieval: It helps in discarding a large number of nonqualifying documents. In this paper two methods for creating signatures are studied analytically, one based on word signatures and the other on superimposed coding. Closed-form formulas are derived for the false-drop probability of the two methods, factors that affect it are studied, and performance comparisons of the two methods based on these formulas are provided.
Cell-Free Fetal DNA in Maternal Blood (2004)

N THIS ISSUE OF THE JOURNAL, THE FINDINGS REPORTED in the study by Dhallan and colleagues 1 on enhancing recovery of cell-free DNA in maternal blood have major clinical implications. Developing a reliable, transportabletechnologyforcell-freeDNAanalysisimpacts2crucial areas—prenatal genetic diagnosis and cancer detection and surveillance. In prenatal genetic diagnosis, detecting a fetal abnormality without an invasive procedure (or with fewer invasive procedures) is a major advantage. Likewise incancersurveillance(eg,inpatientswithleukemia),monitoring treatment without having to perform a bone marrow aspiration for karyotype also would be of great benefit. Prenatal genetic diagnosis has been available in the United Statessince1968,whenchromosomalabnormalitiesandmetabolictraitsproveddetectablebyanalysisofamnioticfluidcells obtainedbyamniocentesis.Themostcommonindicationfor prenatal genetic testing is maternal age older than 35 years; other indications include prior trisomic offspring, balanced parental chromosomal rearrangements, or increased risk for a mendelian trait. The standard approach is to offer women either second-trimester amniocentesis or first-trimester chorionic villus sampling, which are comparable or nearly comparable in safety. The high diagnostic accuracy of these techniques must be balanced against the risks of undergoing an invasiveprocedure. 2 Estimatesforprocedure-relatedfetalloss
Statistical properties of the traditional algorithm-based designs for phase I cancer clinical trials (2001)

Although there are several new designs for phase I cancer clinical trials including the continual reassessment method and accelerated titration design, the traditional algorithm-based designs, like the '3 + 3' design, are still widely used because of their practical simplicity. In this paper, we study some key statistical properties of the traditional algorithm-based designs in a general framework and derive the exact formulae for the corresponding statistical quantities. These quantities are important for the investigator to gain insights regarding the design of the trial, and are (i) the probability of a dose being chosen as the maximum tolerated dose (MTD); (ii) the expected number of patients treated at each dose level; (iii) target toxicity level (i.e. the expected dose-limiting toxicity (DLT) incidences at the MTD); (iv) expected DLT incidences at each dose level and (v) expected overall DLT incidences in the trial. Real examples of clinical trials are given, and a computer program to do the calculation can be found at the authors' website approximately linyo" locator-type="url">http://www2.umdnj.edu/ approximately linyo.
Activity-based probes for the proteomic profiling of metalloproteases (2004)

Metalloproteases (MPs) are a large and diverse class of enzymes implicated in numerous physiological and pathological processes, including tissue remodeling, peptide hormone processing, and cancer. MPs are tightly regulated by multiple posttranslational mechanisms in vivo, hindering their functional analysis by conventional genomic and proteomic methods. Here we describe a general strategy for creating activity-based proteomic probes for MPs by coupling a zinc-chelating hydroxamate to a benzophenone photocrosslinker, which promote selective binding and modification of MP active sites, respectively. These probes labeled active MPs but not their zymogen or inhibitor-bound counterparts and were used to identify members of this enzyme class up-regulated in invasive cancer cells and to evaluate the selectivity of MP inhibitors in whole proteomes. Interestingly, the matrix metalloproteinase inhibitor GM6001 (ilomastat), which is currently in clinical development, was found to also target the neprilysin, aminopeptidase, and dipeptidylpeptidase clans of MPs. These results demonstrate that MPs can display overlapping inhibitor sensitivities despite lacking sequence homology and stress the need to evaluate MP inhibitors broadly across this enzyme class to develop agents with suitable target selectivities in vivo. Activity-based profiling offers a powerful means for conducting such screens, as this approach can be carried out directly in whole proteomes, thereby facilitating the discovery of disease-associated MPs concurrently with inhibitors that selectively target these proteins.
Immunogenicity of Recombinant Protective Antigen and Efficacy against Aerosol Challenge with Anthrax (2005)

Immunization with a recombinant form of the protective antigen (rPA) from Bacillus anthracis has been carried out with rhesus macaques. Rhesus macaques immunized with 25 mug or more of B. subtilis-expressed rPA bound to alhydrogel had a significantly increased immunoglobulin G (IgG) response to rPA compared with macaques receiving the existing licensed vaccine from the United Kingdom (anthrax vaccine precipitated [AVP]), although the isotype profile was unchanged, with bias towards the IgG1 and IgG2 subclasses. Immune macaque sera from all immunized groups contained toxin-neutralizing antibody and recognized all the domains of PA. While the recognition of the N terminus of PA (domains 1 to 3) was predominant in macaques immunized with the existing vaccines (AVP and the U.S. vaccine anthrax vaccine adsorbed), macaques immunized with rPA recognized the N- and C-terminal domains of PA. Antiserum derived from immunized macaques protected macrophages in vitro against the cytotoxic effects of lethal toxin. Passive transfer of IgG purified from immune macaque serum into naive A/J mice conferred protection against challenge with B. anthracis in a dose-related manner. The protection conferred by passive transfer of 500 mug macaque IgG correlated significantly (P = 0.003; r = 0.4) with the titers of neutralizing antibody in donor macaques. Subsequently, a separate group of rhesus macaques immunized with 50 mug of Escherichia coli-derived rPA adsorbed to alhydrogel was fully protected against a target dose of 200 50% lethal doses of aerosolized B. anthracis. These data provide some preliminary evidence for the existence of immune correlates of protection against anthrax infection in rhesus macaques immunized with rPA.
Tetra-O-methyl nordihydroguaiaretic acid inhibits growth and induces death of leukemia cells independent of Cdc2 and survivin (2007)

Tetra-O-methyl nordihydroguaiaretic acid (M4N) was shown to induce G2 arrest and suppress human xenograft tumor growth by inhibiting Cdc2 and survivin. We examined the effect of M4N on leukemia and found that M4N inhibited growth and induced cell death in leukemic cell lines and blasts from AML patients. However, no significant changes in Cdc2 and survivin levels and G2 arrest were observed. Cell death and growth inhibition were dependent neither on XIAP, Bcl-2, and Bcl-X(L) levels nor on caspase-8. M4N did not promote cell differentiation in HL-60 cells. Interestingly, significant inhibition of AKT phosphorylation was observed in M4N treated OCI-AML3 cells. Collectively, our data showed that M4N inhibited cell growth and induced cell death in both leukemic cell lines and AML patient sample via a mechanism not mediated by Cdc2 and survivin inhibition and suggested that the extrinsic and the mitochondrial apoptotic pathways are not essential.
Effects of K+ channel blockers on the anoxic response of CNS myelinated axons (1998)

COMPOUND action potentials (CAPs) from adult rat optic nerves were recorded in vitro. The area under the CAP was compared before and after 1 h anoxia/reoxygenation. Resting compound membrane potential was measured using the cold grease-gap technique. The acute reduction of CAP magnitude by anoxia was unaffected by TEA (20 mM), 4-AP (300 μM), or the KATP blockers glibenclamide (300 μM) and tolbutamide (2 mM). Neither these K+ channel blockers, nor glipizide (100 μM) or the KATP activator diazoxide (500 μM) altered post-anoxic CAP area recovery. In contrast, although Cs+ (5 mM) accelerated anoxic CAP failure and membrane depolarization, this cation significantly increased CAP area recovery post-anoxia from 22 ± 10% (s.d.) to 60 ± 22% (p < 0.0001). The unique effects of Cs+ suggest that inward rectifier channels may play an important role in the induction of anoxic injury in optic nerve axons.
Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models (2017)

The gut microbiota regulates T cell functions throughout the body. We hypothesized that intestinal bacteria impact the pathogenesis of multiple sclerosis (MS), an autoimmune disorder of the CNS and thus analyzed the microbiomes of 71 MS patients not undergoing treatment and 71 healthy controls. Although no major shifts in microbial community structure were found, we identified specific bacterial taxa that were significantly associated with MS. <i>Akkermansia muciniphila</i> and <i>Acinetobacter calcoaceticus</i>, both increased in MS patients, induced proinflammatory responses in human peripheral blood mononuclear cells and in monocolonized mice. In contrast, <i>Parabacteroides distasonis</i>, which was reduced in MS patients, stimulated antiinflammatory IL-10-expressing human CD4<sup>+</sup>CD25<sup>+</sup> T cells and IL-10<sup>+</sup>FoxP3<sup>+</sup> Tregs in mice. Finally, microbiota transplants from MS patients into germ-free mice resulted in more severe symptoms of experimental autoimmune encephalomyelitis and reduced proportions of IL-10<sup>+</sup> Tregs compared with mice "humanized" with microbiota from healthy controls. This study identifies specific human gut bacteria that regulate adaptive autoimmune responses, suggesting therapeutic targeting of the microbiota as a treatment for MS.
Sequence and analysis of the citrulline biosynthetic operon argC-F from Bacillus subtilis (1994)

The citrulline biosynthetic operon argC-F located at 100 degrees on the Bacillus subtilis chromosome contains seven open reading frames which encode all the enzymes required for the biosynthesis of citrulline. The operon is transcribed as a single transcription unit. The second cistron of the operon is homologous to ArgJ (ornithine acetyltransferase) from Bacillus stearothermophilus and Neisseria gonorrhoeae, suggesting that the acetylation of glutamate and the deacetylation of acetylornithine are carried out by a single enzyme in a cyclical pathway. The argF gene is an orthologue of argF from Pseudomonas aeruginosa and a paralogue of arcB from P. aeruginosa and argF/argI from Escherichia coli.
FORRepeats: detects repeats on entire chromosomes and between genomes (2003)

We present a heuristic method, named FORRepeats, which is based on a novel data structure called factor oracle. In the first step it detects exact repeats in large sequences. Then, in the second step, it computes approximate repeats and performs pairwise comparison. We compared its computational characteristics with BLAST and REPuter. Results demonstrate that it is fast and space economical. We show FORRepeats ability to perform intra-genomic comparison and to detect repeated DNA sequences in the complete genome of the model plant Arabidopsis thaliana.
Highly efficient selection of epitope specific antibody through competitive yeast display library sorting (2013)

Combinatory antibody library display technologies have been invented and successfully implemented for the selection and engineering of therapeutic antibodies. Precise targeting of important epitopes on the protein of interest is essential for such isolated antibodies to serve as effective modulators of molecular interactions. We developed a strategy to efficiently isolate antibodies against a specific epitope on a target protein from a yeast display antibody library using dengue virus envelope protein domain III as a model target. A domain III mutant protein with a key mutation inside a cross-reactive neutralizing epitope was designed, expressed, and used in the competitive panning of a yeast display naïve antibody library. All the yeast display antibodies that bound to the wild type domain III but not to the mutant were selectively sorted and characterized. Two unique clones were identified and showed cross-reactive binding to envelope protein domain IIIs from different serotypes. Epitope mapping of one of the antibodies confirmed that its epitope overlapped with the intended neutralizing epitope. This novel approach has implications for many areas of research where the isolation of epitope-specific antibodies is desired, such as selecting antibodies against conserved epitope(s) of viral envelope proteins from a library containing high titer, high affinity non-neutralizing antibodies, and targeting unique epitopes on cancer-related proteins.
Manual Aspiration Thrombectomy (2012)

Manual aspiration thrombectomy is a useful addition to the armamentarium of endovascular treatment modalities for acute stroke.
A Survey of Partitional and Hierarchical Clustering Algorithms (2018)

The two most widely studied clustering algorithms are partitional and hierarchical clustering. These algorithms have been heavily used in a wide range of applications primarily due to their simplicity and ease of implementation relative to other clustering algorithms. Partitional methods need to be provided with a set of initial seeds which are then improved iteratively. Hierarchical clustering can be achieved in two different ways, namely, bottom-up and top-down clustering. Hierarchical methods can start off with the individual data points in single clusters and build the clustering. Hierarchical clustering algorithms approach the problem of clustering by developing a binary tree-based data structure called the dendrogram. Once the dendrogram is constructed, one can automatically choose the right number of clusters by splitting the tree at different levels to obtain different clustering solutions for the same dataset without rerunning the clustering algorithm again.
The effects of repetitive transcranial magnetic stimulation in the treatment of depression (2010)

Repetitive transcranial magnetic stimulation (rTMS) is currently emerging as one of the first fundamentally new treatments in psychiatric practice for a considerable number of years. Research into the use of rTMS for the treatment of patients with depression has now been conducted for over 15 years. The aim of this article was to review the development of rTMS treatment for depression and the current state of evidence supporting its use. The vast majority of the trials conducted on the technique have evaluated the efficacy of high-frequency rTMS applied to the left dorsolateral prefrontal cortex using a set of parameters very similar to those originally described in the mid-1990s. This 'standard' form of rTMS clearly appears to have antidepressant efficacy, and its effects have now been confirmed in several large-scale clinical trials and a number of meta-analyses: response is better than that of sham stimulation, although the number of responders to treatment is relatively modest. A wide range of alternative forms of rTMS have been, or are currently being, evaluated. Low-frequency stimulation applied to the right prefrontal cortex appears to have similar efficacy to standard treatment and it is possible that the bilateral approaches may prove more effective. Novel methods of stimulation, such as priming stimulation, theta-burst stimulation and deep TMS, appear to be promising although require further evaluation. Significant benefit appears likely to accumulate through the use of methods that involve a more reliable targeting of prefrontal brain regions. Research is also required to evaluate the long-term effects of rTMS treatment, its use as a maintenance therapy and to establish reliable predictors of response to treatment.
Quantization of a Friedmann-Robertson-Walker model in N=1 Supergravity with Gauged Supermatter (1995)

The theory of N = 1 supergravity with gauged supermatter is studied in the context of a k = + 1 Friedmann minisuperspace model. It is found by imposing the Lorentz and supersymmetry constraints that there are {\seveni no} physical states in the particular SU(2) model studied.
Demonstration and Diagnostic Significance of Pro-Gastrin-Releasing Peptide in Medullary Thyroid Carcinoma (2000)

The expression of pro-gastrin-releasing peptide (proGRP) in medullary thyroid carcinoma (MTC) and other histological types of thyroid carcinoma was studied by an immunohistochemical technique, using polyclonal anti-proGRP antiserum. Immunoreactivity for proGRP was detected exclusively in MTC (n = 7); other histological types (n = 12) were all negative for proGRP. In addition, serum proGRP levels were elevated in patients with primary or recurrent MTC (n = 3), and they changed in parallel with serum calcitonin (CT), and carcinoembryonic antigen (CEA). These results show that proGRP, which is considered to be a specific marker for small-cell lung carcinoma, may be also a potential tumor marker for MTC, in addition to CT and CEA.
Detection of a decrease in green fluorescent protein fluorescence for the monitoring of cell death: An assay amenable to high-throughput screening technologies (2001)

This novel GFP-based microplate assay combines sensitivity and rapidity, is easily amenable to HTS setups, making it an assay of choice for cytotoxicity evaluation.
Theory of shock wave propagation during laser ablation (2004)

Laser ablation consists of three coupled processes: (i) heat conduction within the solid, (ii) flow through a discontinuity layer (evaporation wave) attached to the solid surface, and (iii) shock wave expansion of the laser induced plume. In this paper, a one-dimensional solution for all three coupled processes is presented. The heat conduction and the evaporation wave are solved numerically. The shock wave expansion of the laser induced plume, however, is solved analytically, to our knowledge, for the first time; analytical solutions for the classic Riemann problem have been employed to solve the transient propagation of the strong shock wave. This model provides a sound theoretical basis for the analysis of the laser ablation process. The temperature, pressure, density, and velocity of the laser induced plume at different laser intensities, back temperatures, back pressures, and ambient gas species are calculated. The effects of the laser intensity, back temperature, back pressure, and ambient gas species are analyzed. The theoretical results provide insight into experimental results available in the literature.
Electroosmosis with step changes in zeta potential in microchannels (2007)

Abstract This article presents an analytical solution for two‐dimensional fluid flow in a rectangular microchannel in the vicinity of a step change in the zeta (ζ) potential. The stream function is determined from the creeping flow approximation to the Navier‐Stokes equations assuming a fixed volumetric axial flow, a constant electric field, and thin symmetric double layers. The resulting biharmonic equation is solved using a double‐sided Laplace transformation, which is then inverted by Heaviside expansion. The resulting series solution provides closed‐form expressions for the velocity and pressure fields that help explain how the recirculating flows generated by an abrupt change in the surface potential may contribute both locally and globally to the hydrodynamic dispersion in straight microchannels. © 2007 American Institute of Chemical Engineers AIChE J, 2007