gebhart/patrepeval huggingface dataset:
Neocartilage Derived from Transplanted Perichondrium (1981)

The articular surfaces of rabbit patellae were completely eburnated and resurfaced with ear perichondrium or fascia lata or left unresurfaced. Both mature and immature animals were used and were sacrificed at 3, 6, and 12 months postoperatively. Only those joints resurfaced with perichondrium formed neocartilage. The neocartilage was composed of variable amounts of chondroitin sulfate; histologic appearances ranged from hyaline cartilage to fibrocartilage to fibrous tissue. Scanning electron microscopy revealed that the neocartilage surface was irregular, fibrillated, and disorganized. Biochemical analyses documented the variability of the neocartilage, one specimen being quite similar to normal articular cartilage. Cell-culture experiments with isolated rabbit periochondrocytes, chondrocytes, and fibroblasts were conducted to determine whether those cell types could produce cartilage matrix in vitro. The ability of sparse cultures of perichondrocytes to synthesize chondroitin sulfate under serum-free conditions is evidence that these cells are unlike fibroblasts and more like chondrocytes in their in vitro behavior. These in vitro and in vivo studies show that perichondrocytes are relatively differentiated cells with the potential to make cartilage. Elucidation of the factors contributing to the variable results of perichondral transplantation is essential before clinical applications will be predictably successful.
Photoacoustic Doppler Effect from Flowing Small Light-Absorbing Particles (2007)

From the flow of a suspension of micrometer-scale carbon particles, the photoacoustic Doppler shift is observed. As predicted theoretically, the observed Doppler shift equals half of that in Doppler ultrasound and does not depend on the direction of laser illumination. This new physical phenomenon provides a basis for developing photoacoustic Doppler flowmetry, which can potentially be used for detecting fluid flow in optically scattering media and especially low-speed blood flow of relatively deep microcirculation in biological tissue.
Effect of glutathione depletion and oral N‐acetyl‐cysteine treatment on CD4 + and CD8 + cells (1994)

HIV-infected individuals and SIV-infected rhesus macaques have, on the average, decreased plasma cysteine and cystine concentrations and decreased intracellular glutathione levels. We show that the cysteine supply and the intracellular glutathione levels have a strong influence on the T cell system. A study of healthy human subjects revealed that persons with intracellular glutathione levels of 20-30 nmol/mg protein had significantly higher numbers of CD4+ T cells than persons with either lower or higher glutathione levels. Persons who moved during a 4-week observation period from the optimal to the suboptimal range (10-20 nmol/mg) experienced, on the average, a 30% decrease in CD4+ T cell numbers. This decrease was prevented by treatment with N-acetyl-cysteine (NAC). NAC caused this relative increase of CD4+ T cell numbers in spite of decreasing glutathione levels and not by increasing the glutathione level. Our studies suggest that the immune system may be exquisitely sensitive not only against a cysteine and glutathione deficiency but also against an excess of cysteine.
Evaluation of c-myc proto-oncogene in primary human breast carcinomas. (1992)

The expression of the c-myc proto-oncogene product was examined by immunohistochemistry in 11 normal breast tissues, 31 invasive and 14 non-invasive breast carcinomas. The c-myc product was detected in all breast carcinoma specimens and in seven of 11 normal breast tissues. Invasive tumors stained more frequently with the anti-myc monoclonal antibody (MAb) than non-invasive tumors, while the level of expression in normal breast tissue was much less than that in a breast cancer. Marked heterogeneity in the c-myc expression was seen among different tumors and within individual tumors. None of the eight invasive tumors with a high protein level of the c-myc showed evidence of gene amplification by Southern blot analysis.
Antibiotic Prophylaxis for Permanent Pacemaker Implantation (1998)

Results of the present meta-analysis suggest that systemic antibiotic prophylaxis significantly reduces the incidence of potentially serious infective complications after permanent pacemaker implantation. They support the use of prophylactic antibiotics at the time of pacemaker insertion to prevent short-term pocket infection, skin erosion or septicemia.
Observations on Fiber-Forming Collagens in the Anulus Fibrosus (2000)

These observations on the location of Types I and II collagen provide a more detailed structural definition of the anulus fibrosus, which may assist in further investigation of discal herniation.
JavaScript developer's resource : client-side programming using HTML, Netscape plug-ins and Java applets (1996)

26792-2 Need to develop professional-quality JavaScript applications? You need this book! If you're a Web site or intranet developer, you need to understand JavaScript, the full-fledged scripting environment that can help you achieve Java-like benefits without becoming an expert Java programmer. That's why you need The JavaScript Developer's Resource, the first end-to-end guide to writing JavaScript applications. The JavaScript Developer's Resource introduces you to every aspect of client-side scripting, including. *All the basics: functions, variables, operators, I/O, and the JavaScript Object Model. *Advanced techniques like forms and event handling. *The JavaScript development environment-including the new Navigator 3.0 browser and Navigator Gold JavaScript interpreter. *Extending JavaScript's power with Java applets and plug-ins. *100s of code samples, tips for optimizing scripts, and gotchas to watch out for!All the JavaScript examples in the book, plus these great Netscape plug-ins: *Macromedia Shockwave (PowerMac, WindowsTM 95 and NT) *Crescendo Plug-in (Mac, WindowsTM 95 and NT) *Adobe Acrobat (Windows, Mac, Sun SPARC, HP-UX) *ToolVox Player (Windows 95, Mac) *Ncompass ActiveX Plug-In (Windows 95 and NT)
High‐intensity focused ultrasound for noninvasive functional neurosurgery (2009)

Transcranial magnetic resonance (MR)-guided high-intensity focused ultrasound (tcMRgHIFU) implies a novel, noninvasive treatment strategy for various brain diseases. Nine patients with chronic neuropathic pain were treated with selective medial thalamotomies. Precisely located thermal ablations of 4mm in diameter were produced at peak temperatures of 51 degrees C to 60 degrees C under continuous visual MR guidance and MR thermometry. The resulting lesions are clearly visible on follow-up MR imaging. All treatments were well tolerated, without side effects or neurological deficits. This is the first report on successful clinical application of tcMRgHIFU in functional brain disorders, portraying it as safe and reliable for noninvasive neurosurgical interventions.
Prevention of postoperative pericardial adhesions by closure of the pericardium with absorbable polymer patches. An experimental study. (1992)

Pericardial adhesions after cardiac operations are a widely known phenomenon. They may severely complicate reoperations, making reentry hazardous, increasing bleeding, and prolonging the operation time. The anatomic orientation and visibility of both bypass grafts and coronary arteries are also impaired. With the aim of minimizing pericardial adhesions after cardiac operations, we studied the course of tissue regeneration after implantation of a new absorbable patch made from poly-hydroxy-butyrate. A total of 23 sheep were studied. Of these, 18 formed the test group and five served as control animals. The animals were killed at intervals of 2 to 30 months after the operation. In 14 of the 18 test animals no adhesions developed. In three animals loose adhesions were found, and in one with signs of postoperative infection there were moderate, generalized adhesions. All control sheep showed moderate adhesions; no infection was noted in this group. Light microscopy in the test group revealed a layer of mesothelium-like cells facing the epicardial side; this was already present in the early specimens. Poly-hydroxy-butyrate appeared to be slowly phagocytosed by polynucleated macrophages, which were still found occasionally in the late samples. Lymphocytes and platelets were rare. Scanning electron microscopy showed, on the epicardial side of the regenerated tissue, a mesothelium-like lining that completely covered the underlying collagen layer. The surface cell morphology grossly resembled that of native pericardium. It was concluded that in this animal model poly-hydroxy-butyrate pericardial patches decreased adhesions and preserved coronary anatomy. The findings in the control group demonstrated that pericardial surgery in the sheep was associated with adhesion formation.
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs (1997)

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
GaN-based diodes and transistors for chemical, gas, biological and pressure sensing (2004)

There is renewed emphasis on development of robust solid-state sensors capable of uncooled operation in harsh environments. The sensors should be capable of detecting chemical, gas, biological or radiation releases as well as sending signals to central monitoring locations. We discuss the advances in use of GaN-based solid-state sensors for these applications. AlGaN/GaN high electron mobility transistors (HEMTs) show a strong dependence of source/drain current on the piezoelectric polarization-induced two-dimensional electron gas (2DEG). Furthermore, spontaneous and piezoelectric polarization-induced surface and interface charges can be used to develop very sensitive but robust sensors to detect gases, polar liquids and mechanical pressure. AlGaN/GaN HEMT structures have been demonstrated to exhibit large changes in source–drain current upon exposing the gate region to various block co-polymer solutions. Pt-gated GaN Schottky diodes and Sc2O3/AlGaN/GaN metal-oxide semiconductor diodes also show large change in forward currents upon exposure to H2. Of particular interest is detection of ethylene (C2H4), which has strong double bonds and hence is difficult to dissociate at modest temperatures. Apart from combustion gas sensing, the AlGaN/GaN heterostructure devices can be used as sensitive detectors of pressure changes. In addition, large changes in source–drain current of the AlGaN/GaN HEMT sensors can be detected upon adsorption of biological species on the semiconductor surface. Finally, the nitrides provide an ideal platform for fabrication of surface acoustic wave (SAW) devices. The GaN-based devices thus appear promising for a wide range of chemical, biological, combustion gas, polar liquid, strain and high temperature pressure-sensing applications. In addition, the sensors are compatible with high bit-rate wireless communication systems that facilitate their use in remote arrays.
Enabling Instantaneous Relocation of Virtual Machines with a Lightweight VMM Extension (2010)

We are developing an efficient resource management system with aggressive virtual machine (VM) relocation among physical nodes in a data center. Existing live migration technology, however, requires a long time to change the execution host of a VM, it is difficult to optimize VM packing on physical nodes dynamically, corresponding to ever-changing resource usage. In this paper, we propose an advanced live migration mechanism enabling instantaneous relocation of VMs. To minimize the time needed for switching the execution host, memory pages are transferred after a VM resumes at a destination host. A special character device driver allows transparent memory page retrievals from a source host for the running VM at the destination. In comparison with related work, the proposed mechanism supports guest operating systems without any modifications to them (i.e, no special device drivers and programs are needed in VMs). It is implemented as a lightweight extension to KVM (Kernel-based Virtual Machine Monitor). It is not required to modify critical parts of the VMM code. Experiments were conducted using the SPECweb2005 benchmark. A running VM with heavily-loaded web servers was successfully relocated to a destination within one second. Temporal performance degradation after relocation was resolved by means of a precaching mechanism for memory pages. In addition, for memory intensive workloads, our migration mechanism moved all the states of a VM faster than existing migration technology.
Influence of Platelets and Platelet Microbicidal Protein Susceptibility on the Fate of Staphylococcus aureus in an In Vitro Model of Infective Endocarditis (2000)

Several lines of evidence indicate that platelets protect against endovascular infections such as infective endocarditis (IE). It is highly likely that a principal mechanism of this platelet host defense role is the release of platelet microbicidal proteins (PMPs) in response to agonists generated at sites of endovascular infection. We studied the ability of platelets to limit the colonization and proliferation of Staphylococcus aureus in an in vitro model of IE. Three isogenic S. aureus strains, differing in their in vitro susceptibility to thrombin-induced platelet microbicidal protein-1 (tPMP), were used: ISP479C (parental strain; highly susceptible to tPMP [tPMP(s)]); ISP479R (transposon mutant derived from ISP479; tPMP resistant [tPMP(r)]); or 757-5 (tPMP(r) transductant of the ISP479R genotype in the ISP479 parental background). Time-kill assays and in vitro IE models were used to examine the temporal relationship between thrombin-induced platelet activation and S. aureus killing. In time-kill studies, early platelet activation (30 min prior to bacterial exposure) correlated with a significant bactericidal effect against tPMP(s) ISP479C (r(2) > 0.90, P < 0.02) but not against tPMP(r) strains, ISP479R or 757-5. In the IE model, thrombin activation significantly inhibited proliferation of ISP479C within simulated vegetations compared to strains ISP479R or 757-5 (P < 0.05). The latter differences were observed despite there being no detectable differences among the three S. aureus strains in initial colonization of simulated vegetations. Collectively, these data indicate that platelets limit intravegetation proliferation of tPMP(s) but not tPMP(r) S. aureus. These findings underscore the likelihood that platelets play an important antimicrobial host defense role in preventing and/or limiting endovascular infections due to tPMP(s) pathogens.
Development of selective aryl hydrocarbon receptor modulators for treatment of breast cancer (1999)

The aryl hydrocarbon receptor (AhR) is a basic helix-loop-helix DNA-binding protein that forms a transcriptionally-active heterodimer with the AhR nuclear translocator (Arnt) protein. The nuclear AhR complex is a ligand-induced transcription factor and the environmental toxicant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a high affinity ligand for the AhR. TCDD induces a diverse spectrum of tissue-, sex- and species-specific biochemical and toxic responses in Ah-responsive cells/tissues including the inhibition of 17β-oestradiol (E2)-induced gene expression in the rodent uterus and mammary and in human breast cancer cell lines. TCDD also inhibits spontaneous and carcinogen-induced mammary tumour formation and growth in rodent models. Research in this laboratory has utilised the AhR as a target for developing anticancer drugs for treatment of breast cancer and two different structural classes of selective AhR modulators (SAhRMs) have been developed. Alternate-substituted (1,3,6,8- and 2,4,6,8-) alkyl polychlorinated dibenzofurans (PCDFs) and substituted diindolylmethanes (DIMs) bind the AhR and induce a pattern of AhR-oestrogen receptor (ER) inhibitory cross-talk similar to that observed for TCDD including inhibition of mammary tumour growth at doses < 1.0 mg/kg/day. In contrast, effective doses of these compounds do not induce hepatic CYP1A1-dependent activity or other AhR-mediated toxic responses induced by TCDD. These results indicate that SAhRMs may be an important new class of drugs for clinical treatment of breast cancer via AhR-ER inhibitory cross-talk.
Vitamin D supplementation in pre-dialysis chronic kidney disease (2012)

Vitamin D deficiency is associated with a variety of skeletal, cardiometabolic, and immunologic co-morbidities that are present in chronic kidney disease (CKD). We performed a systematic review to investigate the effects of vitamin D supplementation, in the form of ergocalciferol or cholecalciferol, on various health outcomes in early CKD. Seventeen clinical trials were identified, only two of which were randomized, placebo controlled trials. The majority of studies supplementing with > 2,000 IU/day of cholecalciferol achieved optimal vitamin D status, whereas studies supplementing with ergocalciferol were less consistent. Studies varied widely in their effects on lowering serum parathyroid hormone concentrations. Few studies investigated effects of vitamin D treatment on other clinical health indicators in early CKD. Rigorous studies are necessary to investigate optimal vitamin D dosing strategies in early CKD for the maintenance of adequate vitamin D status, management of secondary hyperparathyroidism and improvement of non-skeletal related clinical outcomes.
DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present (2014)

Next-generation sequencing (NGS) technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. Escherichia coli DNA polymerase I proteolytic (Klenow) fragment was originally utilized in Sanger's dideoxy chain-terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE) and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage ϕ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, ϕ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies.
Recombinant Adeno-Associated Virus Serotype 2 Vectors Mediate Stable Interleukin 10 Secretion from Salivary Glands into the Bloodstream (2002)

We have constructed a recombinant adeno-associated virus serotype 2 vector encoding human interleukin 10 (rAAVhIL10). IL-10 is a potent antiinflammatory/immune cytokine, which has received growing attention for its therapeutic potential. Human IL-10 (hIL-10) production was virus dose dependent after in vitro infection of HSG cells, a human submandibular gland cell line. The vector-derived hIL-10 produced was biologically active, as the medium from rAAVhIL10-infected HSG cells caused a dose-dependent blockade of IL-12 secretion from spleen cells of IL-10 knockout mice challenged with heat-killed Brucella abortus. Administration of rAAVhIL10 (10(10) genomes per gland) to both mouse submandibular glands led to hIL-10 secretion into the bloodstream (approximately 1-5 pg/ml), that is, in an endocrine manner, which was stable for approximately 2 months. Salivary gland administration of rAAVhIL10 under experimental conditions was more efficacious than intravenous administration (approximately 0.5-0.7 pg/ml). Also, hIL-10 was readily secreted in vitro from organ cultures of minced submandibular glands infected with rAAVhIL10, 6 or 8 weeks earlier. Consistent with these results, hIL-10 mRNA was detected by reverse transcription-polymerase chain reaction in submandibular glands of mice infected with rAAVhIL10 but not from control mice. At these doses, little to no hIL-10 was detected in mouse saliva. Using a rAAV serotype 2 vector encoding beta-galactosidase, we observed that the primary parenchymal target cells were ductal. These findings represent the first report of rAAV use to target exocrine glands for systemic secretion of a therapeutic protein, and support the notion that rAAV serotype 2 vectors may be useful in salivary glands for local (periglandular) and systemic gene-based protein therapeutics.
Attenuating Burn Wound Inflammatory Signaling Reduces Systemic Inflammation and Acute Lung Injury (2006)

The relationship between local inflammation and the subsequent systemic inflammatory response is poorly described. In a burn injury model, the dermal inflammatory response may act as an ongoing trigger for the systemic inflammatory response syndrome (SIRS) and subsequent systemic complications. We hypothesized that topical attenuation of burn wound inflammatory signaling will control the dermal inflammatory source, attenuate SIRS, and reduce acute lung injury. Mice received a 30% total body surface area burn. Subgroups were treated with specific p38 MAPK inhibitor or vehicle, which was topically applied to wounds. Topical p38 MAPK inhibition significantly reduced burn wound inflammatory signaling and subsequent systemic expression of proinflammatory cytokines and chemokines. In vitro macrophage functional assays demonstrated a significant attenuation in serum inflammatory mediators from animals receiving the topical inhibitor. Topical p38 MAPK inhibition resulted in significantly less pulmonary inflammatory response via reduction of pulmonary neutrophil sequestration, pulmonary cytokine expression, and a significant reduction in pulmonary microvascular injury and edema formation. Although dermal activating transcription factor-2, a downstream p38 MAPK target, was significantly reduced, there was no reduction in pulmonary activating transcription factor-2 expression, arguing against significant systemic absorption of the topical inhibitor. These experiments demonstrate a strong interaction between dermal inflammation and systemic inflammatory response. Attenuating local inflammatory signaling appears effective in reducing SIRS and subsequent systemic complications after burn injury.