gebhart/patrepeval huggingface dataset:
<title>Ultrasound-based servoing of manipulators for telesurgery</title> (2002)

Certain minimally invasive surgical procedures involve the treatment of highly precise target locations within deformable tissues. While preoperative MRI and CT models can be used for surgical planning, they provide only coarse guidance during surgery due to their limited resolution and owing to tissue deformation. Ultrasound imaging is a promising means of obtaining real-time intraoperative data for target localization that is particularly well suited to minimally invasive surgery due to its portability, speed, and safety. This paper presents a system, in which ultrasound images are used to guide a manipulator to a surgical site. Electromagnetic tracking of the ultrasound probe is used to orient the images. These are then segmented in real time to determine target locations. Finally, target coordinates are used to produce control inputs to drive the manipulator to the target site. The potential of the approach is demonstrated experimentally using a manipulator arm, phantom target, and commercial ultrasound machine.
Protective effects of anti-Bordetella pertussisadenylate cyclase antibodies against lethal respiratory infection of the mouse (1987)

Experimental respiratory infection of mice with a Bordetella pertussis clone producing and releasing high yields of pertussis toxin and adenylate cyclase was lethal, inducing complete edematous hemorrhagic alveolitis within 48–72 h. By preincubating the challenge inoculum with polyclonal antibodies against the filamentous haemagglutinin (FHA), the pertussis toxin (Ptx), the adenylate cyclase (AC) or a monoclonal anti-AC antibody, we found that only anti-FHA and anti-AC antibodies were protective against the lethal lesions. These results provide direct evidence that B. pertussis AC might be incriminated in the pathogenesis of whooping cough as a major toxin responsible for the local cytopathic syndrome in the respiratory tract.
Synthesis and Characterization of Model Polyalkane−Poly(ethylene oxide) Block Copolymers (1996)

We describe the preparation of a new set of amphiphilic block copolymers with well-defined molecular weights and block volume fractions. The synthesis of a variety of polyalkane−poly(ethylene oxide) block copolymers was accomplished by a new polymerization−hydrogenation sequence. Initially, anionic polymerization of either butadiene or isoprene was performed followed by end capping with ethylene oxide. The resulting hydroxyl-terminated polydienes were catalytically hydrogenated to give the corresponding hydroxyl-terminated polyalkanes. These polymeric alcohols were then titrated with potassium naphthalenide to yield the analogous potassium alkoxides. This type of macroinitiator was employed in the polymerization of ethylene oxide. Seventeen polyalkane−poly(ethylene oxide) block copolymers were prepared in near quantitative yields with molecular weights ranging from (1.4 to 8.7) × 103 and poly(ethylene oxide) volume fractions ranging from 0.29 to 0.73. These polymers are model materials for block copolymer phase behavior studies.
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution (1998)

An excess of nonsynonymous substitutions over synonymous ones is an important indicator of positive selection at the molecular level. A lineage that underwent Darwinian selection may have a nonsynonymous/synonymous rate ratio (dN/dS) that is different from those of other lineages or greater than one. In this paper, several codon-based likelihood models that allow for variable dN/dS ratios among lineages were developed. They were then used to construct likelihood ratio tests to examine whether the dN/dS ratio is variable among evolutionary lineages, whether the ratio for a few lineages of interest is different from the background ratio for other lineages in the phylogeny, and whether the dN/dS ratio for the lineages of interest is greater than one. The tests were applied to the lysozyme genes of 24 primate species. The dN/dS ratios were found to differ significantly among lineages, indicating that the evolution of primate lysozymes is episodic, which is incompatible with the neutral theory. Maximum-likelihood estimates of parameters suggested that about nine nonsynonymous and zero synonymous nucleotide substitutions occurred in the lineage leading to hominoids, and the dN/dS ratio for that lineage is significantly greater than one. The corresponding estimates for the lineage ancestral to colobine monkeys were nine and one, and the dN/dS ratio for the lineage is not significantly greater than one, although it is significantly higher than the background ratio. The likelihood analysis thus confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages.
Optimizing color reproduction of natural images (1998)

The paper elaborates on understanding, measuring and optimizing perceived color quality of natural images. We introduce a model for optimal color reproduction of natural scenes which is based on the assumption that color quality of natural images is constrained by perceived naturalness and colorfulness of these images. To verify the model, a few experimentswere carried out where subjects estimated the perceived &#x2018;naturalness&#x2019;, &#x2018;colorfulness&#x2019; and &#x2018;quality&#x2019; of images of natural scenes. The judgments were related to statistical parameters of the color point distribution across the images in the CIELUV color space. It was found that the perceptually optimal color reproduction can be derived from this statistic within the framework of our model. We specify naturalness, colorfulness and quality indices, describing the observer's judgments. Finally, an algorithm for optimizing perceived quality of color reproduction of natural scenes is discussed.
A Cell Culture Platform to Maintain Long-term Phenotype of Primary Human Hepatocytes and Endothelial Cells (2017)

PHH/fibroblast/endothelial tricultures constitute a robust platform to elucidate reciprocal interactions between PHHs and endothelial cells in physiology, disease, and after drug exposure.
High concentrations of bioactive glass material (BioGran®) vs. autogenous bone for sinus floor elevation (2002)

In this study, high concentrations of bioactive glass (BG) particles were compared with autogenous bone in their capacity to augment maxillary bone when grafted in the human sinus floor using a split mouth design. Three female patients with severe maxillary atrophy underwent bilateral sinus floor elevation and bone grafting using 80-100% BG particles (300-355 microm in size) mixed with 20% to 0% iliac crest bone particles at one (experimental) side, and 100% iliac crest derived bone particles at the other (control) side. A total of 22 bone biopsies was taken at the time of fixture installation; that is, at 4, 6 and 15 months after grafting, and processed for histology and histomorphometry. At the control (autogenous bone) sides, trabecular bone amounted to 39% of the biopsy volume in the graft (site) at 4 months, almost 41% at 6 months, and 42% at 15 months. This bone contained viable osteocytes and was mostly of mature, lamellar type. At the experimental (BG particles) sides, the graft consisted of 27% of mostly woven (and some lamellar) bone at 4 months, 36% (woven and lamellar) bone at 6 months, and 39% (mainly lamellar) bone at 15 months. The grafted BG particles started to excavate at 4 months and their centers gradually filled with bone tissue. As a consequence, the volume of BG particles in the biopsy decreased from 29% at 4 months to 15% at 6 months and 8% at 15 months. The BG particles appeared to resorb within 1-2 years by dissolution rather than by osteoclastic activity. Parameters for bone turnover (% osteoid surface, % resorption surface) indicated that bone remodeling was very active at both experimental and control sides, during more than 6 months. These results suggest that mixtures of mainly (80-90%) BG particles and some (10-20%) autogenous bone are effective for bone regeneration in the augmented sinus offer 6 months healing time, while about 12 months healing time is needed for 100% BG particles.
Effects of MMP2 in migration and proliferation of vessel smooth muscle cells (2006)

Objective To investigate the effects of MMP2 in migration and proliferation of vessel smooth muscle cells(VSMC).Methods The expressions of MMP2 and proliferation of vessel smooth muscle cells were detected by SDS-PAGE Zymography and immunohisto-chemistry,respectively.Results Compared to the control artery,the percentage of proliferating of vessel smooth muscle cells in the injured artery increased to 17.2±3.8% on 3 days and 7.2±1.8% on 7 days in the intimae,P0.05,significant increase of proliferating of vessel smooth muscle cells were also detected in the media(10.3±0.3% on 3 days and 6.24±0.2% on 7 days P0.05).Conclusion MMP2 can enhance migration and proliferation of vessel smooth muscle cells.
cis-Acting Determinants of c-myc mRNA Stability (1990)

Rapid turnover of the c-myc message mediates both the low basal level of mRNA and the rapid response to changes in transcription. The primary RNA instability determinant (RID sequence) resides in the 3' untranslated region (UTR), within an 80 base region that is rich in A and U residues. In contrast to granulocyte-macrophage colony-stimulating factor (GM-CSF) mRNA in which the RID sequence has been mapped to a repeating AUUUA sequence, mutation of the only copy of this sequence in the c-myc 3' UTR has no effect on RNA turnover. Thus the c-myc RID sequence appears to be quite different from that of GM-CSF, which may account for the differential regulation of half-life exhibited by these mRNAs. c-myc mRNA turnover is also tightly coupled to translation since translational inhibitors stabilize this mRNA. Mutation of the initiating AUG to a termination codon stabilizes c-myc RNA, arguing that loading with polysomes (perhaps accompanied by localization on the cytoskeleton) is also required for proper message turnover.
Don't sit on the fence: A static analysis approach to automatic fence insertion (2013)

Modern architectures rely on memory fences to prevent undesired weakenings of memory consistency. As the fences' semantics may be subtle, the automation of their placement is highly desirable. But precise methods for restoring consistency do not scale to deployed systems code. We choose to trade some precision for genuine scalability: our technique is suitable for large code bases. We implement it in our new musketeer tool, and detail experiments on more than 350 executables of packages found in Debian Linux 7.1, e.g. memcached (about 10000 LoC).
The molecular structures of divinyl sulfide and divinyl sulfoxide in the gas phase from electron diffraction (1993)

The molecular geometries and conformations of divinyl sulfide (DVS). (CH2CH)2S, and divinyl sulfoxide (DVSO), (CH2CH)2SO, have been determined by gas-phase electron diffraction and vibrational analysis. The CC bonds tend to eclipse other bonds or a sulfur lone pair in the free molecules. The only conformer found in the vapours of DVS at room temperature has no symmetry and is characterized by dihedral angles C–S–CC of 32(9)° and –148(7)°; both CH2 groups lie on the same side of the C–S–C plane. This form is very similar to the prevailing form of divinyl ether.8 DVSO is a mixture of conformers. The form present in 78(17)% at 82 °C has C–S–CC of 121(4)° and –121(4)° and Cssymmetry; both CC bonds eclipse the SO bonds. Intramolecular O ⋯ H(C) interactions of about 2.5 Å seem to stabilize existing conformers of DVSO. Important parameters are (rg with estimated total errors), for DVS: S–C 1.758(4), CC 1.342(3), C–H 1.092(3). (C·H)mean(within a CH2CH group) 2.108(6)Å, C–S–C 101.8(21)°, S–CC 123.7(6)°; for DVSO: SO 1.477(3), S–C 1.785(4). CC 1.330(3), C–H 1.091(5), (C·H)mean 2.141(10)Å, C–SO 107.5(14)°, C–S–C 99.2(18)°, S–CC 118.5(8)°. Bond lengths do not indicate effects of conjugation in these molecules.
Graphics computer-aided receptor mapping as a predictive tool for drug design: development of potent, selective, and stereospecific ligands for the 5-HT1A receptor (1988)

A conformational study of four 5-HT1A (serotonin) receptor ligands ((R-(-)-methiothepin, spiperone, (S)-(-)-propranolol, and buspirone) led to the definition of a pharmacophore and a three-dimensional map of the 5-HT1A antagonist recognition site. These models were used to design new compounds and successfully predict their potency, stereospecificity, and selectivity. For example, 8-[4-[(1,4-benzodioxan-2-ylmethyl)amino] butyl]-8-azaspiro[4.5]decane-7,9-dione (1, MDL 72832) has nanomolar affinity (pIC50 = 9.14) for the 5-HT1A binding site in rat frontal cortex. As predicted, the S-(-) enantiomer of 1 was more active than its R-(+) enantiomer (pIC50 = 9.21 and 7.66, respectively) and a naphthalene analogue of 1 displayed the expected improved selectivity.
TRAIL Receptor-Selective Mutants Signal to Apoptosis via TRAIL-R1 in Primary Lymphoid Malignancies (2005)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and its agonistic antibodies, which are currently in early clinical trials for treating various malignancies, induce apoptosis through triggering of either TRAIL-R1 or TRAIL-R2. Based on studies using agonistic monoclonal antibodies, we recently proposed that primary chronic lymphocytic leukemic cells seem to signal apoptosis primarily through TRAIL-R1. We have now synthesized mutant forms of TRAIL specific for TRAIL-R1 or TRAIL-R2. The selectivity of these mutants to induce apoptosis in cell lines is due to selective binding to their cognate receptors resulting in apoptosis via formation of a death-inducing signaling complex. Using these mutants, we now unequivocally show that primary cells from patients with chronic lymphocytic leukemia and mantle cell lymphoma signal to apoptosis almost exclusively through TRAIL-R1. Thus, no significant therapeutic benefit can be anticipated from treating such patients with agents currently in clinical trials that signal predominantly through TRAIL-R2, such as HGS-ETR2 or Apo2L/TRAIL. Our study highlights the necessity to determine whether primary cells from a particular tumor signal via TRAIL-R1 or TRAIL-R2. Such information will provide a rational approach to optimize TRAIL therapy.
Detecting Faulty Nodes with Data Errors for Wireless Sensor Networks (2014)

Wireless Sensor Networks (WSN) promise researchers a powerful instrument for observing sizable phenomena with fine granularity over long periods. Since the accuracy of data is important to the whole system's performance, detecting nodes with faulty readings is an essential issue in network management. As a complementary solution to detecting nodes with functional faults, this article, proposes FIND, a novel method to detect nodes with data faults that neither assumes a particular sensing model nor requires costly event injections. After the nodes in a network detect a natural event, FIND ranks the nodes based on their sensing readings as well as their physical distances from the event. FIND works for systems where the measured signal attenuates with distance. A node is considered faulty if there is a significant mismatch between the sensor data rank and the distance rank. Theoretically, we show that average ranking difference is a provable indicator of possible data faults. FIND is extensively evaluated in simulations and two test bed experiments with up to 25 MicaZ nodes. Evaluation shows that FIND has a less than 5% miss detection rate and false alarm rate in most noisy environments.
Introduction: Strategies for Developing Genetically Modified Mice (2010)

Advancements in transgenic technologies have made the mouse one of the most useful animal models for biomedical research. Several technological breakthroughs have allowed the generation transgenic and knockout mouse models some 25 years ago. Subsequently, the technology has undergone many improvements, advancing our ability to control the expression of the genes and determine the cell types where the genetic modification should take place. Hence, the mouse is unique in offering the possibility to understand genotype-phenotype relationships that are relevant for unraveling the biological role of these genes in the human. This chapter provides an introductory overview.
Recruitment of Endogenous Stem Cells for Tissue Repair (2008)

The traditional concept of stem cell therapy envisions the isolation of stem cells from patients, propagation and differentiation in vitro, and subsequent re-injection of autologous cells into the patient. There are many problems associated with this paradigm, particularly during the in vitro manipulation process and the delivery and local retention of re-injected cells. An alternative paradigm that could be easier, safer, and more efficient, would involve attracting endogenous stem cells and precursor cells to the defect site for new tissue regeneration. Hepatocyte growth factor (HGF), a pleiotropic cytokine of mesenchymal origin, exerts a strong chemoattractive effect on mesenchymal stem cells (MSCs) and neural stem cells (NSCs), and induces migration of MSCs in vitro. However, HGF undergoes rapid proteolysis in vivo, which results in a very short lifetime of the bioactive cytokine. To maintain the therapeutic level of HGF at the defect site necessary for endogenous stem cell recruitment, sustained, long-term, and localized delivery of HGF is required. Thiol-modified glycosaminoglycans hyaluronan (HA) and heparin (HP), combined with modified gelatin (Gtn), have been crosslinked with poly(ethylene glycol) diacrylate (PEGDA) to afford semisynthetic ECM-like (sECM) hydrogels that can both provide controlled growth factor release and permit cell infiltration and proliferation. Herein we compare the use of different sECM compositions for controlled release of HGF and concomitant recruitment of human bone marrow MSCs into the scaffold in vitro. [Figure: see text].
[Treatment of familial erythermalgia with the association of lidocaine and mexiletine]. (2003)

Primary familial erythermalgia is highly resistant to treatment. The combined action of lidocain and mexiletine, usually well tolerated (class IB antiarrythmic), blocks the sodium channels. The mechanism of action of their analgesic effect is peripheral or central or even mixed. This benefit warrants confirmation in other forms of erythermalgia.
Tunable liquid-filled microlens array integrated with microfluidic network (2003)

An elastomer-based tunable liquid-filled microlens array integrated on top of a microfluidic network is fabricated using soft lithographic techniques. The simultaneous control of the focal length of all the microlenses composing the elastomeric array is accomplished by pneumatically regulating the pressure of the microfluidic network. A focal length tuning range of hundreds of microns to several millimeters is achieved. Such an array can be used potentially in dynamic imaging systems and adaptive optics.
A Processive Single-Headed Motor: Kinesin Superfamily Protein KIF1A (1999)

A single kinesin molecule can move "processively" along a microtubule for more than 1 micrometer before detaching from it. The prevailing explanation for this processive movement is the "walking model," which envisions that each of two motor domains (heads) of the kinesin molecule binds coordinately to the microtubule. This implies that each kinesin molecule must have two heads to "walk" and that a single-headed kinesin could not move processively. Here, a motor-domain construct of KIF1A, a single-headed kinesin superfamily protein, was shown to move processively along the microtubule for more than 1 micrometer. The movement along the microtubules was stochastic and fitted a biased Brownian-movement model.
Is Telomere Length a Biomarker of Aging? A Review (2010)

Telomeres, the DNA-protein structures located at the ends of chromosomes, have been proposed to act as a biomarker of aging. In this review, the human evidence that telomere length is a biomarker of aging is evaluated. Although telomere length is implicated in cellular aging, the evidence suggesting telomere length is a biomarker of aging in humans is equivocal. More studies examining the relationships between telomere length and mortality and with measures that decline with "normal" aging in community samples are required. These studies would benefit from longitudinal measures of both telomere length and aging-related parameters.
Recent progress and challenges in drug development to fight hand, foot and mouth disease (2019)

<b>Introduction</b>: Hand, foot and mouth disease (HFMD) is a serious public health concern in the Asia-Pacific region with recurrent cyclical outbreaks. Enterovirus 71 (EV-A71) and coxsackievirus type A are the main causative agents of HFMD. While majority of HFMD cases are mild and self-limiting, neurological complications have been reported for EV-A71 associated HFMD. There is currently no effective treatment against HFMD and monovalent vaccines against EV-A71 are currently limited to the Chinese market.<b>Areas covered</b>: As of today, HFMD antiviral development has focused on EV-A71 and involves conventional screening of drug libraries. In recent years, attention has shifted toward identifying druggable host factors to avoid drug resistance and identify drug candidates with broader antiviral activity across EV-A71 genogroups and other HFMD causative agents.<b>Expert opinion</b>: The effective development of HFMD interventions requires us to address the gaps in our understanding of its pathogenesis at the molecular level. The limited resources devoted to the development of HFMD treatment strategies worldwide also contribute to the slow progress of promising drug and vaccine candidates along the clinical pipeline.
Limited Proteolysis of Human α2-HS Glycoprotein/Fetuin (1996)

alpha2-HS glycoprotein is a major protein of human plasma whose function is still obscure. A proteolytically processed form of alpha2-HS glycoprotein lacking a segment of 40 amino acid residues bridging its heavy and light chain portions ("connecting peptide") has been described suggesting that this peptide is released by post-translational processing to fulfill biological role(s) of alpha2-HS glycoprotein. To test this hypothesis we investigated how the connecting peptide is released from the parental molecule by limited proteolysis. We developed monoclonal antibodies to various portions of the connecting peptide and its NH2-terminal flanking region which cross-react with the native alpha2-HS glycoprotein. Purified alpha2-HS glycoprotein from human plasma was subjected to limited proteolysis by proteinases including trypsin, chymotrypsin, elastase plasmin, kallikrein, thrombin, and renin. Immunoprint analysis of the proteolytic digests indicated that alpha2-HS glycoprotein is readily cleaved in its connecting peptide region. NH2-terminal amino sequence analysis of the generated fragments demonstrated that a single proteinase, chymotrypsin, cleaves the critical Leu-Leu bond flanking the NH2-terminal portion of the connecting peptide region. Most but not all of the other proteinase cleavage sites map to a short stretch of 9 residues located in the center portion of the connecting peptide region. Immunoprint analysis of plasma samples from patients with sepsis demonstrate that the connecting peptide region is cleaved under pathological conditions. Our results indicate that the connecting peptide and/or fragments thereof are readily releasable from alpha2-HS glycoprotein in vitro and in vivo.