gebhart/patrepeval huggingface dataset:
Algorithm-based treatment of major depression in an outpatient clinic: clinical correlates of response to a specific serotonin reuptake inhibitor and to triiodothyronine augmentation (2003)

Clinicians who treat major depression are faced with a bewildering choice of antidepressants. Given that all have a lag period before they are effective, choice of the right antidepressant can potentially minimize the duration of symptoms, reduce cost and enhance compliance. Unfortunately, there is very little evidence upon which to base such a decision. We developed a treatment algorithm for non-psychotic, unipolar major depression, and applied it in our clinic. It includes progression from a specific serotonin reuptake inhibitor (SSRI), usually fluoxetine, from a dose of 20 mg to a dose of 40 mg in patients who do not respond. Non-responders to this dose receive augmentation with triiodothyronine (T3, 25-50 microg). All interventions are for fixed time periods and guided by overall clinical improvement as defined by the Clinical Global Inventory. Ninety patients commenced open-label treatment with 20 mg SSRI (fluoxetine, n=81; paroxetine, n=9). Seventy-four patients completed 4 wk of treatment and 44 (48.9%) were responders (intent to treat analysis). Raising the SSRI dose to 40 mg for a further 2 wk was effective in only 5 patients (16.6%). Non-responders to SSRI were significantly more depressed at baseline as reflected by their rating scales scores. Addition of T3 was effective in 10 out of 16 women (62.5%) while none of the 9 males responded. Although values were within the normal range, patients who responded to T3 had higher serum thyroid-stimulating hormone levels than those who did not. Our experience with algorithm-based treatment of unipolar, non-psychotic major depression in outpatients suggests that more than 40% of patients will not respond to initial treatment with an SSRI even when the dose is increased to 40 mg/d; that severity of depression may be an important predictor of response and that T3 may be useful as an augmenter of response in SSRI non-responders but may be less effective in men than in women. The effect of T3 may be related to thyroid function even within the normal range.
Analysis of Pulpal Reactions to Restorative Procedures, Materials, Pulp Capping, and Future Therapies (2002)

Every year, despite the effectiveness of preventive dentistry and dental health care, 290 million fillings are placed each year in the United States; two-thirds of these involve the replacement of failed restorations. Improvements in the success of restorative treatments may be possible if caries management strategies, selection of restorative materials, and their proper use to avoid post-operative complications were investigated from a biological perspective. Consequently, this review will examine pulp injury and healing reactions to different restorative variables. The application of tissue engineering approaches to restorative dentistry will require the transplantation, replacement, or regeneration of cells, and/or stimulation of mineralized tissue formation. This might solve major dental problems, by remineralizing caries lesions, vaccinating against caries and oral diseases, and restoring injured or replacing lost teeth. However, until these therapies can be introduced clinically, the avoidance of post-operative complications with conventional therapies requires attention to numerous aspects of treatment highlighted in this review.
Link adaptation and channel prediction in wireless OFDM systems (2003)

Link adaptation algorithms enhance. throughput in OFDM communication systems by adjusting various transmission parameters based on channel state information. In wireless OFDM systems, however, changes in the channel due to Doppler spread and limits on the reverse link bandwidth make it difficult to fully adapt to current channel conditions. Therefore in this paper we study link adaptation based on time-frequency blocks. We propose an algorithm that adapts the modulation scheme in a time-frequency block to maximize throughput while maintaining a target average block error rate. We describe a channel prediction algorithm and comment on the channel conditions where it improves performance. Simulations show that it is possible to optimize the size of the time-frequency block to maximize throughput given a fixed frequency of link adaptation control messages.
Inexpensive optical tweezers for undergraduate laboratories (1999)

Single beam gradient force optical traps, or tweezers, are a powerful tool for a wide variety of experiments in physics, chemistry, and biology. We describe how to build an optical tweezer with a total cost of ≈$6500 using only commercially available optics and mounts. We also suggest measurements that could be made using the apparatus.
Influence of epidermal permeability barrier disruption and Langerhans' cell density on allergic contact dermatitis. (1997)

Previously, we have showed that artificial epidermal permeability barrier disruption leads to an increase in epidermal Langerhans' cell (LC) density within 24 h. We now asked if this is accompanied by an enhancement of allergic contact dermatitis. Barrier disruption was induced by acetone on the upper arms in 6 volunteers with known sensitization to nickel, fragrance mix, or p-phenylenediamine. Twenty-four hours after this treatment the relevant allergen was applied without occlusion or with Finn chambers. Twenty-four hours after application of the allergen, clinical grading and transepidermal water loss (TEWL) measurements were performed and biopsies were taken. Immunohistochemical stainings for LCs (anti-CD1a, Leu6) and for epidermal proliferation (Ki-S3) were performed. Open applications of the allergens after acetone pretreatment resulted in strong allergic test reactions. TEWL, which showed a 70% recovery 24 h after acetone treatment, was increased again 4-fold by the allergic test reactions. LC density, which was increased by 80% 24 h after acetone-induced barrier disruption, was further enhanced 2.4-fold in total. Epidermal proliferation showed a 6-fold increase after open application of the allergens. Under patch test conditions after acetone pretreatment very strong bullous reactions were observed. We conclude that the increase in epidermal LC density induced by epidermal permeability barrier disruption is accompanied by an enhanced response in allergic contact dermatitis.
A New Design of a Submicropositioner Utilizing Electromagnetic Actuators and Flexure Mechanism (2009)

In this paper, a novel <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">XY</i> -dimensional submicropositioner, including mechanism, control, and analysis, is successfully presented. The design of the submicropositioner utilizes a monolithic parallel flexure mechanism with built-in electromagnetic actuators and optical sensors to achieve the object of 3-DOF precise motion. From the provided experimental results, there are several main goals that have been achieved in this paper: (1) to integrate the electromagnetic actuator and the parallel flexure mechanism for planar positioning system; (2) to establish the mathematical modeling; (3) to develop an advanced adaptive sliding-mode controller; and (4) to perform extensive experiments to test the realistic performance.
Expression and Association of the Yersinia pestis Translocon Proteins, YopB and YopD, Are Facilitated by Nanolipoprotein Particles (2016)

Yersinia pestis enters host cells and evades host defenses, in part, through interactions between Yersinia pestis proteins and host membranes. One such interaction is through the type III secretion system, which uses a highly conserved and ordered complex for Yersinia pestis outer membrane effector protein translocation called the injectisome. The portion of the injectisome that interacts directly with host cell membranes is referred to as the translocon. The translocon is believed to form a pore allowing effector molecules to enter host cells. To facilitate mechanistic studies of the translocon, we have developed a cell-free approach for expressing translocon pore proteins as a complex supported in a bilayer membrane mimetic nano-scaffold known as a nanolipoprotein particle (NLP) Initial results show cell-free expression of Yersinia pestis outer membrane proteins YopB and YopD was enhanced in the presence of liposomes. However, these complexes tended to aggregate and precipitate. With the addition of co-expressed (NLP) forming components, the YopB and/or YopD complex was rendered soluble, increasing the yield of protein for biophysical studies. Biophysical methods such as Atomic Force Microscopy and Fluorescence Correlation Spectroscopy were used to confirm that the soluble YopB/D complex was associated with NLPs. An interaction between the YopB/D complex and NLP was validated by immunoprecipitation. The YopB/D translocon complex embedded in a NLP provides a platform for protein interaction studies between pathogen and host proteins. These studies will help elucidate the poorly understood mechanism which enables this pathogen to inject effector proteins into host cells, thus evading host defenses.
Experimental human muscle pain and muscular hyperalgesia induced by combinations of serotonin and bradykinin (1999)

In the present study, we assessed the muscle pain and possible development of muscular hyperalgesia to mechanical stimuli after two subsequent intramuscular infusions of serotonin (5-HT) and bradykinin (BKN). The pain intensity after the infusions was continuously scored on a visual analogue scale (VAS). The subjects drew the distribution of the pain areas on a map. Pressure pain thresholds (PPTs) and suprapressure pain thresholds (SPPTs) stimulations as 150% of the pre-infusion PPTs were assessed with a pressure algometer at the injection site (10 cm below the patella), at the ankle, and at the contralateral leg and ankle. Skin sensibility was assessed with a Von Frey hair at the same sites. This was done before and after an infusion into the tibialis anterior (TA) muscle on the right leg in ten volunteers. The first infusion in each combination was either serotonin (20 nmol) or isotonic saline (NaCl 0.9%). The second infusion was bradykinin (5 or 10 nmol) or isotonic saline. The two infusions were given over 20 s and separated by 3 min. The isotonic saline followed by BKN did not induce muscle pain or muscular hyperalgesia. However, the combination of 5-HT and BKN (10 nmol) produced: (1) significantly higher VAS scores (P < 0.05) compared with all other combinations; (2) significantly longer pain offset (P < 0.05) compared with the combinations of isotonic saline and BKN; (3) significantly lower PPTs at 5, 20, and 40 min post-infusion (P < 0.05) compared with baseline PPT and PPTs after all other combinations. Cutaneous sensibility to mechanical stimuli and SPPTs were not affected by any of the combinations. The combinations of serotonin and bradykinin produce experimental muscle pain and muscular hyperalgesia to mechanical stimuli. Pre-treatment with serotonin may enhance the effect of bradykinin in the generation of muscle pain and muscular hyperalgesia in humans.
A hypervariable locus D16S309 located at the distal end of 16p (1992)

Probe MS205 was detected by probe 33.15 (1) in a lambda L47. 1 library of MboI digested, size fractionated DNA (5 -20kbp) pooled from 20 unrelated individuals (2).The 5. 1kbp insert was subcloned into the BamHI site of pUC 13 resulting in the subclone pMS205.2which was propagated in E.coli strain DH5a (BRL).Polymorphism: pMS205.2detects a hypervariable locus in genomic DNA digested with MboI and Hinfl revealing DNA fragments 4-7kbp and 2 -Skbp in length respectively.It cannot be detected in HaellI, RsaI or HpaII genomic digests as these enzymes cut within the minisatellite repeat unit.Heterozygosity: The D16S309 locus has multiple alleles and a heterozygosity of 96% or 97 % among 202 unrelated Caucasians and 204 unrelated Afro-Caribbeans tested respectively.Chromosome Localization: The D16S309 locus has been assigned to chromosome 16 by hybridization of the probe pMS205.2to a human-rodent somatic cell hybrid panel of DNAs and to 16p by linkage analysis, where it is closely linked to the 3' and 5' HVRs of the ce-globin locus which is located approximately 145kbp from the telomere of 16p (3).Mendelian Inheritance: Co-dominant inheritance of the MboI DNA fragments detected by pMS205.2 has been shown among the 40 reference families of the CEPH panel.Other Comments: The D16S309 locus has a germline mutation rate to new length alleles of 0.004 per gamete, estimated from 257 families where maternity and paternity have been verified.
Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site (2011)

Precise RNA processing is fundamental to all small RNA-mediated interference pathways. In prokaryotes, clustered, regularly interspaced, short palindromic repeats (CRISPR) loci encode small CRISPR RNAs (crRNAs) that protect against invasive genetic elements by antisense targeting. CRISPR loci are transcribed as a long precursor that is cleaved within repeat sequences by CRISPR-associated (Cas) proteins. In many organisms, this primary processing generates crRNA intermediates that are subject to additional nucleolytic trimming to render mature crRNAs of specific lengths. The molecular mechanisms underlying this maturation event remain poorly understood. Here, we defined the genetic requirements for crRNA primary processing and maturation in Staphylococcus epidermidis. We show that changes in the position of the primary processing site result in extended or diminished maturation to generate mature crRNAs of constant length. These results indicate that crRNA maturation occurs by a ruler mechanism anchored at the primary processing site. We also show that maturation is mediated by specific cas genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci.
Non-intrusive, out-of-band and out-of-the-box systems monitoring in the cloud (2014)

The dramatic proliferation of virtual machines (VMs) in datacenters and the highly-dynamic and transient nature of VM provisioning has revolutionized datacenter operations. However, the management of these environments is still carried out using re-purposed versions of traditional agents, originally developed for managing physical systems, or most recently via newer virtualization-aware alternatives that require guest cooperation and accessibility. We show that these existing approaches are a poor match for monitoring and managing (virtual) systems in the cloud due to their dependence on guest cooperation and operational health, and their growing lifecycle management overheads in the cloud. In this work, we first present Near Field Monitoring (NFM), our non-intrusive, out-of-band cloud monitoring and analytics approach that is designed based on cloud operation principles and to address the limitations of existing techniques. NFM decouples system execution from monitoring and analytics functions by pushing monitoring out of the targets systems' scope. By leveraging and extending VM introspection techniques, our framework provides simple, standard interfaces to monitor running systems in the cloud that require no guest cooperation or modification, and have minimal effect on guest execution. By decoupling monitoring and analytics from target system context, NFM provides ``always-on'' monitoring, even when the target system is unresponsive. NFM also works ``out-of-the-box'' for any cloud instance as it eliminates any need for installing and maintaining agents or hooks in the monitored systems. We describe the end-to-end implementation of our framework with two real-system prototypes based on two virtualization platforms. We discuss the new cloud analytics opportunities enabled by our decoupled execution, monitoring and analytics architecture. We present four applications that are built on top of our framework and show their use for across-time and across-system analytics.
[The clinical response to interferon-gamma in a patient with chronic granulomatous disease and brain abscesses due to Aspergillus fumigatus]. (2000)

Chronic granulomatous disease (CGD) is an heterogeneous inherited disorder where the microbicidal phagocytic properties of leukocytes are impaired. Patients with CGD are prone to severe ious with many microorganisms such as Aspergillus spp (1,2). Recently, interferon gamma (IFN-8) which significantly reduces the frequency of infections in these patients, has been proved useful (3,4). We present our experience with the clinical use of these cytoscine. A 26-year-old woman with CGD suffered recement multiple brain abscesses by Aspergillus fumigatus treated in many occasions with surgical drainage. Since treatment with IFN-8 was started, two years ago, she is well and asymptomatic until the moment.
O4‐11‐02: Towards a small molecule inhibitor of tau exon 10 splicing: Identification of compounds that stabilise the 5'‐splice site stem‐loop (2012)

Silent mutations in the tau exon 10 5'-splice site are associated with certain cases of frontotemporal dementia with Parkinsonism where increased expression of tau containing four microtubule binding domains (4R-Tau) occurs. These mutations modulate splicing by altering the stability of a putative stem-loop structure, which acts as a splice regulatory element (TauSRE). Mutations that destabilise the TauSRE cause increased expression of 4R-Tau; stabilising mutations reduce 4R-Tau expression. This suggests that small molecules, which stabilise TauSRE, would serve as therapeutics for the treatment of tauopathies where 4R-Tau is elevated. To identify small molecules that interact with the TauSRE, we generated the first ever TauSRE Dynamic Atomic-scale RNA drug Target (DART) which was virtually screened with ∼200K small molecules. The DART was generated by selecting TauSRE structures from a conformational pool of 300K produced using molecular dynamics simulations. NMR data were measured for the TauSRE and used to select a smaller ensemble of TauSRE structures. Compounds selected from the virtual screen were investigated for their effects on TauSRE thermal stability using a fluorescence-based assay and a tau-tat minigene cell-based assay. TauSRE containing destabilising or stabilising mutations caused the predicted changes in TauSRE thermal stability and exon 10 splicing. Exon 10 splicing was also inhibited in the cell-based assay using an antisense oligonucleotide directed to the TauSRE. Both known RNA-binding compounds and novel compounds were identified that caused significant stabilisation of the exon 10 stem-loop in the fluorescent assay but failed to show a corresponding reduction in splicing in the cell-based assay. Compound NC11813 stabilised TauSRE by 7oC at 100Î¼M and showed activity in cell based assays, however exon 10 inclusion was increased. The reasons for the lack of correlation between the thermal stability and cell assay data with NC11813 are unclear, but could be related to the thermal stability assay conditions, the presence of competing cellular RNAs and macromolecules, or different binding mechanisms in cell-free and cell-based environments; those possibilities will be discussed. Nonetheless, these results represent to our knowledge the first example of a small molecule identified using a virtual screen to TauSRE, capable of altering RNA splicing.
Enzymatic properties of the Caenorhabditis elegans Dna2 endonuclease/helicase and a species-specific interaction between RPA and Dna2 (2005)

In both budding and fission yeasts, a null mutation of the DNA2 gene is lethal. In contrast, a null mutation of Caenorhabditis elegans dna2+ causes a delayed lethality, allowing survival of some mutant C.elegans adults to F2 generation. In order to understand reasons for this difference in requirement of Dna2 between these organisms, we examined the enzymatic properties of the recombinant C.elegans Dna2 (CeDna2) and its interaction with replication-protein A (RPA) from various sources. Like budding yeast Dna2, CeDna2 possesses DNA-dependent ATPase, helicase and endonuclease activities. The specific activities of both ATPase and endonuclease activities of the CeDna2 were considerably higher than the yeast Dna2 (approximately 10- and 20-fold, respectively). CeDna2 endonuclease efficiently degraded a short 5' single-stranded DNA tail (<10 nt) that was hardly cleaved by ScDna2. Both endonuclease and helicase activities of CeDna2 were stimulated by CeRPA, but not by human or yeast RPA, demonstrating a species-specific interaction between Dna2 and RPA. These and other enzymatic properties of CeDna2 described in this paper may shed light on the observation that C.elegans is less stringently dependent on Dna2 for its viability than Saccharomyces cerevisiae. We propose that flaps generated by DNA polymerase delta-mediated displacement DNA synthesis are mostly short in C.elegans eukaryotes, and hence less dependent on Dna2 for viability.
Tumor necrosis factor: an updated review of its biology. (1993)

TNF plays a major role in the pathogenesis of the septic shock syndrome. TNF exerts a range of beneficial and injurious effects that may ultimately lead to organ dysfunction and death. The burst of TNF release after endotoxemia promotes the progression of the shock syndrome even in the absence of further TNF release. New therapies targeted to the attenuation of TNF may hold promise for the management of patients with septic shock syndrome.
Development of Empirical Temperature and Humidity-Based Degraded-Condition Indicators for Low-Tonnage Air Conditioners (1997)

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Spinodal decomposition in gels (1999)

We construct a Ginzburg-Landau model for gels undergoing spinodal decomposition in terms of the polymer volume fraction and a deformation tensor. We numerically demonstrate that the domain growth is extremely slowed down in late stages, where the surface tension force, which drives the coarsening in usual fluids, is cancelled by the elastic force. The patterns closely resemble those observed in highly viscoelastic, asymmetric binary mixtures.
Cesium reversibly suppresses HeLa cell proliferation by inhibiting cellular metabolism (2017)

The aim of the present study was to investigate the influence of Cs<sup>+</sup> on cultured human cells. We find that HeLa cell growth is suppressed by the addition of 10 mm CsCl into the culture media. In the Cs<sup>+</sup> -treated cells, the intracellular Cs<sup>+</sup> and K<sup>+</sup> concentrations are increased and decreased, respectively. This leads to a decrease in activity of the glycolytic enzyme pyruvate kinase, which uses K<sup>+</sup> as a cofactor. Cs<sup>+</sup> -treated cells show an intracellular pH shift towards alkalization. Based on these results, CsCl presumably suppresses HeLa cell proliferation by inducing an intracellular cation imbalance that affects cell metabolism. Our findings may have implications for the use of Cs<sup>+</sup> in cancer therapy.