gebhart/patrepeval huggingface dataset:
Active tremor compensation in handheld instrument for microsurgery (2004)

Human's ability to perform precise micromanipulation is limited by small involuntary movements inherent to normal hand motion. Microsurgery is one area where the surgeons' performance is hampered by this manual imprecision. Not only that it complicates many delicate surgical procedures, it also makes certain types of intervention impossible. The most familiar type of erroneous movement affecting a healthy person is physiological tremor. 
Instead of going with the more familiar approach of using a teleoperated robotic system, we adopted a less obtrusive and much cheaper approach of implementing accuracy enhancement within a completely handheld tool. This device senses its own motion, distinguishes the erroneous motion from the intended motion, and manipulates its own tip in real time to compensate the erroneous motion. 
This dissertation focuses on the sensing and compensation of the erroneous motion, while tremor modeling and estimation is performed by a previously developed weighted-frequency Fourier linear combiner (WFLC) algorithm. 
Instantaneous motion of the instrument is sensed by a new magnetometer-aided all-accelerometer inertial measurement unit (IMU). The sensing system consists of three dual-axis miniature accelerometers and a three-axis magnetometer. The redundancy in sensing provides two sources of orientation and position information. The angular motion information derived from the differential sensing kinematics algorithm has very high sensing resolution but suffers from integration drift; on the other hand, the orientation obtained from the gravity and magnetic North vectors is noisy but non-drifting. These two complementary sensing sources are fused via an augmented state quaternion-based Kalman filter to yield high quality sensing. 
The instrument tip is manipulated by a three DOF parallel manipulator driven by piezoelectric actuators. The hysteretic non-linearity of the piezoelectric actuator is modeled and linearized by a rate-dependent Prandtl-Ishlinskii operator. Based on the dynamic hysteresis model, an open-loop inverse feedfoward controller is implemented to accurately track dynamic motion profiles. 
While the targeted application of this dissertation is in microsurgery, the principles of the approach is universal and can be extended to other micromanipulation tasks, such as cell manipulation in the biotech industry, gun-sights or handheld military tracking equipment, and handheld video photography etc.
A Mechanism for TCP-Friendly Transport-Level Protocol Coordination (2002)

In this paper, we identify an emerging and important application class comprised of a set of processes on a cluster of devices communicating to a remote set of processes on another cluster of devices across a common intermediary Internet path. We call these applications cluster-tocluster applications,orC-to-C applications. The networking requirements of C-to-C applications present unique challenges. Because the application involves communication between clusters of devices, very few streams will share a complete end-to-end path. At the same time, network performance needs to be measured globally across all streams for the application to employ interstream adaptation strategies. These strategies are important for the application to achieve its global objectives while at the same time realizing an aggregate flow behavior that is congestion controlled and responsive. We propose a mechanism called the Coordination Protocol (CP) to provide this ability. In particular, CP makes fine-grained measurements of current network conditions across all associated flows and provides transport-level protocols with aggregate available bandwidth information using an equation-based congestion control algorithm. A prototype of CP is evaluated within a network simulator and is shown to be effective.
Identifying areas of ecotourism in Northern Ontario: Application of a Geographical Information System Methodology (1994)

Ecotourism has become one of the most rapidly growing forms of tourism in recent years and has spread from primarily tropical areas to a wide range of environments. This expansion has often taken place without appropriate evaluation of destination areas as to their suitability for ecotourism. This paper discusses a methodology for identifying areas with the potential for ecotourism in the context of Northern Ontario. The authors discuss the application of the methodology in a sample study area in Northern Ontario, and evaluate the findings and implications.
Heteroarotinoids Inhibit Head and Neck Cancer Cell Lines in Vitro and in Vivo Through Both RAR and RXR Retinoic Acid Receptors (1999)

A class of less toxic retinoids, called heteroarotinoids, was evaluated for their molecular mechanism of growth inhibition of two head and neck squamous cell carcinoma (HNSCC) cell lines SCC-2 and SCC-38. A series of 14 heteroarotinoids were screened for growth inhibition activity in vitro. The two most active compounds, one that contained an oxygen heteroatom (6) and the other a sulfur heteroatom (16), were evaluated in a xenograph model of tumor establishment in nude mice. Five days after subcutaneous injection of 10(7) SCC-38 cells, groups of 5 nu/nu mice were gavaged daily (5 days/week for 4 weeks) with 20 mg/kg/day of all-trans-retinoic acid (t-RA, 1), 10 mg/kg/day of 6, 10 mg/kg/day of 16, or sesame oil. After a few days, the dose of t-RA (1) was decreased to 10 mg/kg/day to alleviate the side effects of eczema and bone fracture. No significant toxic effects were observed in the heteroarotinoid groups. All three retinoids caused a statistically significant reduction in tumor size as determined by the Student t-test (P < 0. 05). Complete tumor regression was noted in 3 of 5 mice treated with t-RA (1), 4 of 5 mice treated with 16, 1 of 5 mice treated with 6, and 1 of 5 mice treated with sesame oil. Reverse transcriptase polymerase chain reaction (RT-PCR) was used to determine that the expression levels of RARalpha, RXRalpha, and RXRbeta were similar in the two cell lines, while RARbeta expression was higher in SCC-2 over SCC-38, and RARgamma expression was higher in SCC-38 over SCC-2. Receptor cotransfection assays in CV-1 cells demonstrated that 16 was a potent activator of both RAR and RXR receptors, while 6 was selective for the RXR receptors. Transient cotransfection assays in CV-1 cells using an AP-1 responsive reporter plasmid demonstrated that t-RA (1), 6, and 16 each inhibited AP-1-driven transcription in this cell line. In conclusion, the growth inhibition activity of the RXR-selective 6 and the more potent growth inhibition activity of the RAR/RXR pan-agonist 16 implicate both RARs and RXRs in the molecular mechanism of retinoid growth inhibition. Moreover, the chemoprevention activity and the lack of toxicity of heteroarotinoids demonstrate their clinical potential in head and neck cancer chemoprevention.
Heightened susceptibility to secondary traumatization: A meta-analysis of gender differences. (2014)

Although secondary traumatization has been extensively studied, gender difference in susceptibility has received limited attention. This study addressed the issue by a meta-analysis of published findings on male and female persons in close, extended relationships with trauma victims, namely, their spouses, parents, children, and therapists. The analysis included peer-reviewed studies, written in English and published between 1990 and January 2012. Twelve studies reporting 17 findings on 1,623 subjects were identified. All the studies showed females' higher susceptibility to secondary traumatization, with a mean effect size of 0.48 (95% CI [0.35, 0.60]). Moderator analysis revealed that studies conducted in the United States reported lower gender discrepancies than studies conducted elsewhere. The consistent finding that females are considerably more susceptible to secondary traumatization than males means that professionals must be made aware of the special vulnerability of girls and women and help them adopt ways of caring for the traumatized family member or clients while maintaining their own psychological boundaries.
Multiple gamma-crystallins of the mouse lens: fractionation of mRNAs by cDNA cloning. (1982)

cDNAs made from polyadenylylated RNAs of the mouse lens were cloned by the G.C tailing procedure in the bacterial plasmid pBR322. Four recombinant DNAs containing gamma-crystallin sequences were identified by hybrid selection and translation. Sequence analysis of the in vivo-labeled gamma-crystallin polypeptides that cofocused isoelectrically with the hybrid-selected translation products established that the four cloned cDNAs were derived from mRNAs encoding gamma-crystallin polypeptides with similar NH2 termini. The cDNA clones had different restriction maps and could discriminate among the different gamma-crystallin mRNAs under stringent hybridization conditions. Under relaxed hybridization conditions, the cDNA clones cross-hybridized with all gamma-crystallin mRNAs, and even slightly with beta-crystallin mRNAs, as judged by in vitro translation. RNA blot hybridization showed that the mouse lens gamma-crystallin mRNAs are 840 +/- 100 nucleotides long. These data indicate that there are at least four similar gamma-crystallin mRNAs and suggest (but do not establish) the existence of a closely related family of gamma-crystallin genes.
N-Glycolylneuraminic Acid Xenoantigen Contamination of Human Embryonic and Mesenchymal Stem Cells Is Substantially Reversible (2006)

Human embryonic and mesenchymal stem cell therapies may offer significant benefit to a large number of patients. Recently, however, human embryonic stem cell lines cultured on mouse feeder cells were reported to be contaminated by the xeno-carbohydrate N-glycolylneuraminic acid (Neu5Gc) and considered potentially unfit for human therapy. To determine the extent of the problem of Neu5Gc contamination for the development of stem cell therapies, we investigated whether it also occurs in cells cultured on human feeder cells and in mesenchymal stem cells, what are the sources of contamination, and whether the contamination is reversible. We found that N-glycolylneuraminic acid was present in embryonic stem cells cultured on human feeder cells, correlating with the presence of Neu5Gc in components of the commercial serum replacement culture medium. Similar contamination occurred in mesenchymal stem cells cultured in the presence of fetal bovine serum. The results suggest that the Neu5Gc is present in both glycoprotein and lipid-linked glycans, as detected by mass spectrometric analysis and monoclonal antibody staining, respectively. Significantly, the contamination was largely reversible in the progeny of both cell types, suggesting that decontaminated cells may be derived from existing stem cell lines. Although major complications have not been reported in the clinical trials with mesenchymal stem cells exposed to fetal bovine serum, the immunogenic contamination may potentially be reflected in the viability and efficacy of the transplanted cells and thus bias the published results. Definition of safe culture conditions for stem cells is essential for future development of cellular therapies.
Therapeutic anti-EGFR antibody 806 generates responses in murine de novo EGFR mutant–dependent lung carcinomas (2007)

Activating EGFR mutations occur in human non-small cell lung cancer (NSCLC), with 5% of human lung squamous cell carcinomas having EGFRvIII mutations and approximately 10%-30% of lung adenocarcinomas having EGFR kinase domain mutations. An EGFR-targeting monoclonal antibody, mAb806, recognizes a conformational epitope of WT EGFR as well as the truncated EGFRvIII mutant. To explore the anticancer spectrum of this antibody for EGFR targeted cancer therapy, mAb806 was used to treat genetically engineered mice with lung tumors that were driven by either EGFRvIII or EGFR kinase domain mutations. Our results demonstrate that mAb806 is remarkably effective in blocking EGFRvIII signaling and inducing tumor cell apoptosis, resulting in dramatic tumor regression in the EGFRvIII-driven murine lung cancers. Another EGFR-targeting antibody, cetuximab, failed to show activity in these lung tumors. Furthermore, treatment of murine lung tumors driven by the EGFR kinase domain mutation with mAb806 also induced significant tumor regression, albeit to a less degree than that observed in EGFRvIII-driven tumors. Taken together, these data support the hypothesis that mAb806 may lead to significant advancements in the treatment of the population of NSCLC patients with these 2 classes of EGFR mutations.
Development of a Long-Acting Insulin Analog Using Albumin Fusion Technology (2005)

The primary therapeutic goal for the treatment of diabetes is maintenance of a long-term, near-normoglycemic condition and prevention of the onset or progression of the complications associated with the disease. Although several analogs of human insulin have been developed, the currently prescribed long-acting insulin analogs do not provide a stable basal glycemia for more than a few hours. Here, we report the development of Albulin, a long-acting insulin analog obtained by direct gene fusion of a single-chain human insulin to human serum albumin. Albulin showed an elimination t(1/2) of approximately 7 h in normoglycemic mice. In vitro pharmacodynamic profiles for Albulin characterized by receptor binding, inhibition of gluconeogenesis, induction of glucose uptake, and global regulation of gene expression in relevant cell types showed that Albulin produced similar activity profiles compared with that of recombinant human insulin. A single Albulin administration in vivo normalized blood glucose level in diabetic mice in a relatively peakless and sustained (24-h) fashion. A further reduction in glucose levels was achieved by administering a recombinant human insulin a few hours after Albulin injection in mice, indicating the potential for Albulin therapy in combination with available fast-acting insulin derivatives. In summary, Albulin displays characteristics of a potent long-acting insulin analog that can be evaluated for use as a novel insulin therapy for patients with insulin-dependent diabetes.
T-DNA Mutagenesis in Arabidopsis (2003)

Insertional mutagenesis is a basic genetic tool that allows for a rapid identification of the tagged genes responsible for a particular phenotype. Transposon and Agrobacterium-mediated DNA integration are the most commonly used biological mutagens in plants. The main drawback of these technologies is the relatively low frequency of mutations, as compared to those induced by conventional chemical or physical agents, thus limiting the use of insertional mutagens to the generation of large mutant populations in few genetic backgrounds. Recent improvements in Agrobacterium-mediated transformation efficiency and an increasing repertoire of transformation vectors available to the research community is making this type of mutagen very attractive for individual laboratories interested in the studies of mutations in particular genetic backgrounds. Herein, we describe a simple yet robust Arabidopsis transformation procedure that can be used to generate large numbers of insertional mutants in Arabidopsis thaliana. Using this protocol, transformation efficiencies of up to 5% can be achieved.
Effects of Topical H-7 on Outflow Facility, Intraocular Pressure, andCorneal Thickness in Monkeys (2004)

Five percent H-7 increases outflow facility and decreases IOP, but does not affect corneal thickness. Multiple doses of H-7 induce greater reduction of IOP than a single dose. The effect of H-7 on IOP may be pressure dependent. Clinical Relevance Multiple topical treatments with low doses of H-7 or analogues may substantially reduce outflow resistance in the hypertensive eye without meaningfully affecting the cornea.
Intratracheal exposure to multi-walled carbon nanotubes induces a nonalcoholic steatohepatitis-like phenotype in C57BL/6J mice (2014)

The effects of multi-walled carbon nanotubes (MWCNTs) exposure have garnered great interest in the field of public health, due to the high aspect ratio of MWCNTs. Because of worldwide increases in obesity prevalence, nonalcoholic fatty liver disease (NAFLD) is now the most common prevalent liver disease and is considered to be a component of metabolic syndrome, which is a cluster of disorders that also includes dyslipidemia, diabetes mellitus, arteriosclerosis, and hypertension. Exposure to MWCNTs is known to be a risk factor for lung and cardiovascular diseases, but its effect on NAFLD is unknown. In this study, we investigated the effects of intratracheal exposure of two different types of MWCNTs, namely, pristine multi-walled carbon nanotubes (PMWCNTs) and acid-treated multi-walled carbon nanotubes (TMWCNTs), on liver pathogenesis. Direct instillation of a test material into the lungs has been employed as a quantitatively reliable alternative method of inhalation exposure. The 10% weight loss dose was assessed in three months of subchronic study and is defined here as the maximum tolerated dose (MTD) of PMWCNTs and TMWCNTs; by this metric, MTD for a 1-year exposure of MWCNTs was determined to be 0.1 mg/mouse. Mice exposed to PMWCNTs and TMWCNTs for one year developed a nonalcoholic steatohepatitis (NASH)-like phenotype, characterized by inflammation, hepatic steatosis, and fibrosis. Furthermore, PMWCNTs induced a more severe NASH-like phenotype than TMWCNTs, which was related to consistent up-regulation of interleukin (IL)-6 and plasminogen activator inhibitor (PAI)-1. Impaired cholesterol homeostasis, overexpression of NF-κBp65, and suppression of peroxisome proliferator-activated receptor gamma (PPARγ) in the liver were also observed.
Identification of New Flagellar Genes ofSalmonella entericaSerovar Typhimurium (2006)

RNA levels of flagellar genes in eight different genetic backgrounds were compared to that of the wild type by DNA microarray analysis. Cluster analysis identified new, potential flagellar genes, three putative methyl-accepting chemotaxis proteins, STM3138 (McpA), STM3152 (McpB), and STM3216(McpC), and a CheV homolog, STM2314, in Salmonella, that are not found in Escherichia coli. Isolation and characterization of Mud-lac insertions in cheV, mcpB, mcpC, and the previously uncharacterized aer locus of S. enterica serovar Typhimurium revealed them to be controlled by sigma28-dependent flagellar class 3 promoters. In addition, the srfABC operon previously isolated as an SsrB-regulated operon clustered with the flagellar class 2 operon and was determined to be under FlhDC control. The previously unclassified fliB gene, encoding flagellin methylase, clustered as a class 2 gene, which was verified using reporter fusions, and the fliB transcriptional start site was identified by primer extension analysis. RNA levels of all flagellar genes were elevated in flgM or fliT null strains. RNA levels of class 3 flagellar genes were elevated in a fliS null strain, while deletion of the fliY, fliZ, or flk gene did not affect flagellar RNA levels relative to those of the wild type. The cafA (RNase G) and yhjH genes clustered with flagellar class 3 transcribed genes. Null alleles in cheV, mcpA, mcpB, mcpC, and srfB did not affect motility, while deletion of yhjH did result in reduced motility compared to that of the wild type.
A mutated beta-catenin gene encodes a melanoma-specific antigen recognized by tumor infiltrating lymphocytes. (1996)

A number of antigens recognized by tumor-reactive T cells have recently been identified. The antigens identified in mouse model systems appear, with one exception, to represent the products of mutated genes. In contrast, most of the antigens recognized by human tumor-reactive T cells reported to date appear to represent the products of non-mutated genes. Here we report the isolation of a cDNA clone encoding beta-catenin, which was shown to be recognized by the tumor-infiltrating lymphocyte (TIL) 1290, a HLA-A24 restricted melanoma-specific CTL line from patient 888. The cDNA clone, which was isolated from the autologous melanoma cDNA library, differed by a single base pair from the published beta-catenin sequence, resulting in a change from a serine to a phenylalanine residue at position 37. Normal tissues from this patient did not express the altered sequence, nor did 12 allogeneic melanomas, indicating that this represented a unique mutation in this patient's melanoma. A peptide corresponding to the sequence between amino acids 29 and 37 of the mutant gene product was identified as the T cell epitope recognized by TIL 1290. The observation that HLA-A24 binding peptides contain an aromatic or hydrophobic residue at position 9 suggested that the change at position 37 may have generated a peptide (SYLDSGIHF) which was capable of binding to HLA-A24, and a competitive binding assay confirmed this hypothesis. The beta-catenin protein has been shown previously to be involved in cell adhesion mediated through the cadherin family of cell surface adhesion molecules. The high frequency of mutations found in members of cellular adhesion complexes in a variety of cancers suggests that these molecules may play a role in development of the malignant phenotype.
Closed-form blind channel identification and source separation in SDMA systems through correlative coding (1998)

We address the problem of blind identification of multiuser multiple-input multiple-output (MIMO) finite-impulse response (FIR) digital systems. This problem arises in spatial division multiple access (SDMA) architectures for wireless communications. We present a closed-form, i.e., noniterative, consistent estimator for the MIMO channel based only on second-order statistics. To obtain this closed form we introduce spectral/correlation asymmetry between the sources by filtering each source output with adequate correlative filters. Our algorithm uses the closed form MIMO channel estimate to cancel the intersymbol interference (ISI) due to multipath propagation and to discriminate between the sources at the wireless base station receiver. Simulation results show that, for single-user channels, this technique yields better channel estimates in terms of mean-square error (MSE) and better probability of error than a well-known alternative method. Finally, we illustrate its performance for MIMO channels in the context of the global system for mobile communications (GSM) system.
The Irish Education System and the Economy (2000)

This article summarizes McDonagh’s remarks at the June 14, 1999 Maine Governor’s Economic Development Conference. He outlines Ireland’s educational strategies and investments of the past 30 years, as well as plans for the future, which include not only new educational initiatives but also significant investments in research and development. The educational roots of Ireland’s economic miracle include a concerted national effort to increase participation rates in higher education and a strategic effort to match the country’s education and training programs to the skills needs of global, high-tech companies. Such efforts have spanned decades, have required substantial investment, and have been sustained across changes in government administrations. Most importantly, such efforts have paid off. Ireland boasts one of the most highly skilled workforces in the world and is able to build economic success from its human capital by attracting the inward investment of growing high-tech, global companies.