gebhart/patrepeval huggingface dataset:
The Eocene macrofossil floras of Australia. (1996)

RNA molecules can easily adopt alternative structures in response to different environmental conditions. As a result, a molecule's energy landscape is rough and can exhibit a multitude of deep basins. In the absence of a high-resolution structure, small-angle X-ray scattering data (SAXS) can narrow down the conformational space available to the molecule and be used in conjunction with physical modeling to obtain high-resolution putative structures to be further tested by experiments. Because of the low resolution of these data, it is natural to implement the integration of SAXS data into simulations using a coarse-grained representation of the molecule, allowing for much wider searches and faster evaluation of SAXS theoretical intensity curves than with atomistic models. We present here the theoretical framework and the implementation of a simulation approach based on our coarse-grained model HiRE-RNA combined with SAXS evaluations "on-the-fly" leading the simulation toward conformations agreeing with the scattering data, starting from partially folded structures as the ones that can easily be obtained from secondary structure prediction-based tools. We show on three benchmark systems how our approach can successfully achieve high-resolution structures with remarkable similarity with the native structure recovering not only the overall shape, as imposed by SAXS data, but also the details of initially missing base pairs.
Two-dimensional free-space beam steering with an optical phased array on silicon-on-insulator (2011)

We demonstrate a 16-channel, independently tuned waveguide surface grating optical phased array in silicon for two dimensional beam steering with a total field of view of 20° x 14°, beam width of 0.6° x 1.6°, and full-window background peak suppression of 10 dB.
A Toll-Like Receptor 2 Pathway Regulates the Ppargc1a/b Metabolic Co-Activators in Mice with Staphylococcal aureus Sepsis (2011)

Activation of the host antibacterial defenses by the toll-like receptors (TLR) also selectively activates energy-sensing and metabolic pathways, but the mechanisms are poorly understood. This includes the metabolic and mitochondrial biogenesis master co-activators, Ppargc1a (PGC-1α) and Ppargc1b (PGC-1β) in Staphylococcus aureus (S. aureus) sepsis. The expression of these genes in the liver is markedly attenuated inTLR2(-/-) mice and markedly accentuated in TLR4(-/-) mice compared with wild type (WT) mice. We sought to explain this difference by using specific TLR-pathway knockout mice to test the hypothesis that these co-activator genes are directly regulated through TLR2 signaling. By comparing their responses to S. aureus with WT mice, we found that MyD88-deficient and MAL-deficient mice expressed hepatic Ppargc1a and Ppargc1b normally, but that neither gene was activated in TRAM-deficient mice. Ppargc1a/b activation did not require NF-kβ, but did require an interferon response factor (IRF), because neither gene was activated in IRF-3/7 double-knockout mice in sepsis, but both were activated normally in Unc93b1-deficient (3d) mice. Nuclear IRF-7 levels in TLR2(-/-) and TLR4(-/-) mice decreased and increased respectively post-inoculation and IRF-7 DNA-binding at the Ppargc1a promoter was demonstrated by chromatin immunoprecipitation. Also, a TLR2-TLR4-TRAM native hepatic protein complex was detected by immunoprecipitation within 6 h of S. aureus inoculation that could support MyD88-independent signaling to Ppargc1a/b. Overall, these findings disclose a novel MyD88-independent pathway in S. aureus sepsis that links TLR2 and TLR4 signaling in innate immunity to Ppargc1a/b gene regulation in a critical metabolic organ, the liver, by means of TRAM, TRIF, and IRF-7.
CD28-Deficient Mice Are Highly Resistant to Collagen-Induced Arthritis (1999)

CD28 provides a critical costimulatory signal in Ag-specific T cell activation. Recent studies have revealed an important role for CD28 in the development of autoimmune diseases. We have examined the role of CD28 in collagen-induced arthritis (CIA) by inducing CIA in CD28-deficient DBA/1 mice. CD28-deficient mice never developed arthritis and showed markedly decreased levels of IgG and IgM anti-type II collagen (CII) Abs. In addition, the CD28+/- mice had similar levels of IgG1 and IgG2a anti-CII Abs, whereas in the CD28-deficient mice the level of IgG1 anti-CII Abs was decreased compared with that of IgG2a. IFN-gamma production by lymph node cells in response to CII was also reduced. CD28-deficient mice were either immunized four times with CII in CFA to augment Ag loading or given low doses of IL-12 to enhance Thl type responses. Both treatments resulted in a very low incidence of CIA development and minimal disease. CD28-deficient mice developed arthritis from injection of lymph node cells from CII-immunized wild-type mice, followed by immunization with CII in CFA. Taken together, these results indicate that costimulation of CD28 cannot be replaced by repeated activation through TCR or other costimulatory molecules. Thus, CD28 plays a critical role in both cellular and humoral immunity against CII and is indispensable for the development of CIA.
Shape-Specific, Monodisperse Nano-Molding of Protein Particles (2008)

Herein we report nano-molding proteins for the fabrication of protein PRINT particles of monodisperse size and shape. Lyophilized protein particles are generally highly dispersed in particle size, aggregated, and often made through costly and complicated processes. Attempts to engineer monodisperse, discrete protein particles using wet-milling, spray-freeze-drying, microemulsion, or super critical fluid methods have realized little success. The PRINT technology enables a gentle, facile route to monodisperse particles of 100% protein as small as 200 nm cylinders. Protein PRINT particles of any shape and size are effortlessly achievable. Our research efforts include making PRINT particles composed of albumin and albumin 0.5 wt % siRNA, and Abraxane, the gold standard therapeutic used in metastatic breast cancer.
Minimally Differentiated Acute Myeloid Leukemia (AML-M0): Comparison of 25 Cases With Other French-American-British Subtypes (1997)

We compared the immunophenotypic and karyotypic features of 25 cases of minimally differentiated acute myeloid leukemia (AML-M0) with those of 247 cases comprising all AML French-American-British (FAB) classification. Myeloperoxidase (MPO) was detectable with a specific monoclonal antibody in all cases of AML-M0, whereas CD13 and CD33 were both negative in 4 of the 25 cases. Thus, anti-MPO reliably detects minimal myeloid differentiation in AML-M0. CD34 and terminal deoxynucleotidyl transferase (TdT) were more frequently expressed in AML-M0 (96% and 68% of the cases, respectively) than in the other FAB subsets (P < .001 for both). By contrast, GP-170 and CD7 were less frequently expressed in AML-M0 than in FAB classes such as M1, M4, and M5 (P = .02 and .003, respectively). A total of 80% of AML-M0 cases carried lymphoid markers (including TdT), and 48% showed a coordinate positivity for two or more of them. CD2, CD5, CD10, and CD19 were expressed in a similar fashion among the different FAB groups, whereas CD4 expression was significantly more frequent in AML-M0, AML-M4, and AML-M5 (P = .014). AML-M0 was characterized by a more frequent occurrence of complex karyotypes. In addition, approximately 20% of cases had TdT positivity, complex karyotypes, and anomalies of chromosome 5 and/or 7, a pattern not observed in the other FAB subsets. Finally, 80% of anomalies of chromosome 5 and/or 7 in AML-M0 were comprised within complex karyotypes, whereas only 13% of the remaining FAB cases carried this feature. In summary, AML-M0 frequently expresses immunophenotypic and karyotypic aspects that are likely to identify a "stem cell" pattern.
Total Synthesis of (−)‐Decarbamoyloxysaxitoxin (2007)

A facile and general synthetic strategy for saxitoxin derivatives has been developed, as exemplified by the efficient synthesis of (−)-decarbamoyloxysaxitoxin ((−)-doSTX), the putative enantiomer of the natural product, in 17 steps and in 10 % overall yield. The synthesis features a diastereoselective 1,3-dipolar cycloaddition and a direct oxidation with o-iodoxybenzoic acid (IBX; see scheme, Cbz=benzyloxycarbonyl).
Biology of the Syndecans: A Family of Transmembrane Heparan Sulfate Proteoglycans (1992)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Progesterone concentration in milk and blood serum and reproductiveefficiency of cows after Ovsynch treatment (2016)

An experiment was conducted to investigate the effects of hormonal synchronization of ovulation on progesterone concentrations in milk and blood serum and on reproductive performance. Sixty Holstein-Friesian cows averaging 8000 L over 305 days of lactation were divided into 2 groups of 30 animals. One-factor ANOVA and a t-test of progesterone concentrations in venous serum and milk revealed that the lowest concentrations of progesterone in milk (Ovsynch 5.8 1.0 ng/mL; control 4.5 0.6 ng/mL) and blood serum (Ovsynch 1.3 0.9 ng/mL; control 1.4 0.5 ng/mL) in both groups were found on the day of estrus or artificial insemination (AI) (both P < 0.05). Increases in the concentrations of progesterone in milk (Ovsynch 17.6 4.3 ng/mL; control 10.5 1.9 ng/mL) and blood serum (Ovsynch 3.6 1.1 ng/mL; control 4.0 1.0 ng/mL) were observed on day 7 after AI (both P < 0.05). Concentrations of progesterone in milk and blood serum in nonpregnant cows were reduced on day 21 after AI. Assessment of reproductive performance revealed that the application of treatment shortened the duration of the service period (Ovsynch 76 days; control 83 days) and the calving interval (Ovsynch 376 days; control 382 days).
Ischemia–reperfusion injury stimulates gelatinase expression and activity in kidney glomeruli (2005)

Although ischemia remains the leading cause of acute renal failure in humans, there is little information on the expression and activities of gelatinases of kidney glomeruli during ischemia-reperfusion injury. In this study, we used a unilateral ischemia-reperfusion model to investigate the activity and expression of gelatinases in glomeruli during acute ischemia. Unilateral ischemia was induced in rats by vascular clamping (30 min) followed by reperfusion (60 min) and isolation of glomeruli. The activity and expression of gelatinase proteins were determined by gelatin zymography and Western blotting. Gelatinase mRNA levels were evaluated by reverse transcriptase-PCR. Ischemia and reperfusion increased serum creatinine levels, hallmark of acute renal failure. Ischemia induced mRNA and protein MMP-2 expression. There was strong stimulation of MMP-9 mRNA, both forms of dimeric MMP-9, and active monomeric MMP-9. In contrast to TIMP-1 decreasing, TIMP-2 protein and mRNA increased during ischemia. During reperfusion, there was a gradual reversal of the MMP-2 and MMP-9 levels and a strong inhibition of TIMP-1 and TIMP-2 at the protein and mRNA levels. Endocytic receptor LRP was increased during ischemia and returned to normal during reperfusion. Expression of MMP-9 docking receptor CD-44 was increased during reperfusion. Finally, ZO-1, an in vivo MMP-9 substrate, was degraded during ischemia, revealing that MMP-9 upregulated during ischemia was functional. Our data suggest that stimulation of gelatinase activity during ischemia could contribute to glomeruli injury, providing new therapeutic targets for acute renal failure in humans. In contrast, elevated monomeric MMP-9 activity due to TIMP-1 decrease during reperfusion may participate to glomerular recovery.
Effects of a Hemoglobin-Based Oxygen Carrier (HBOC-201) on Hemodynamics and Oxygen Transport in Patients Undergoing Preoperative Hemodilution for Elective Abdominal Aortic Surgery (1996)

We conducted a pilot study to evaluate the effects of HBOC-201, a bovine hemoglobin-based oxygen carrier, on hemodynamics and oxygen transport in patients undergoing preoperative hemodilution for elective abdominal aortic surgery. After induction of anesthesia and isovolemic hemodilution with 1 L of lactated Ringer's solution, 13 patients were randomly assigned to receive, within 30 min, 3 mL/kg of either HBOC-201 or 6% hydroxyethyl starch (HES). Monitored variables included invasive arterial and pulmonary artery pressures, arterial and mixed venous blood gases, and calculations of cardiac index (CI), systemic and pulmonary vascular resistance indices, oxygen delivery index (DO2I), oxygen consumption index (VO2I), and oxygen extraction ratio (O2ER). Thirty minutes after HBOC-201 infusion, mean arterial pressure, systemic vascular resistance index, and CI were 149% (P = 0.028), 169% (P = 0.046), and 75% (P = 0.46) of the preinfusion values, respectively. No significant changes were noticed in heart rate and pulmonary vascular resistance index. DO2I and VO2I, 30 min after the infusion of HBOC-201, were 79% (P = 0.046) and 76% (P = 0.028) of the preinfusion values, respectively, whereas CaO2 and O2ER remained unaffected. We conclude that HBOC-201, at a dose of 3 mL/kg, impairs oxygen delivery because of adverse effects on cardiac output.
Isolation and characterization of the CYP71D16 trichome-specific promoter from Nicotiana tabacum L. (2002)

Trichomes are specialized epidermal cells that produce secretions that are thought to provide a first line of defence against pests and pathogens. Many trichome-secreted compounds are used commercially as flavourings, medicines, etc. Described here is the cloning and characterization of the promoter of a tobacco trichome-specific P450 gene, CYP71D16. This promoter is shown to direct the specific expression of the reporter gene, beta-glucuronidase (GUS), in glandular trichomes of Nicotiana tabacum cv. T.I. 1068 at all developmental stages. With the full promoter, GUS activity was predominantly in the gland cell, with less in the stalk cell adjacent to the gland, and in lower stalk cells. GUS staining was also observed in the most distal trichome stalk cells of non-glandular trichomes found on variety T.I. 1112. Promoter deletion analysis revealed that the region from -223 to +111 bp is sufficient to direct trichome-specific expression, but not strong gland expression. Examination of the literature suggests that this is the first characterized trichome-specific-promoter shown to function at all stages of plant development. This promoter may provide efficient bioengineering to enhance pest and pathogen resistance, and for molecular farming based on the trichome gland system.
A spectrally constrained dual-band normalization technique for protoporphyrin IX quantification in fluorescence-guided surgery (2012)

We report a dual-band normalization technique for in vivo quantification of the metabolic biomarker, protoporphyrin IX (PpIX), during brain tumor resection procedures. The accuracy of the approach was optimized in tissue simulating phantoms with varying absorption and scattering properties, validated with fluorimetric assessments on ex vivo brain tissue, and tested on human data acquired in vivo during fluorescence-guided surgery of brain tumors. The results demonstrate that the dual-band normalization technique allows PpIX concentrations to be accurately quantified by correction with reflectance data recorded and integrated within only two narrow wavelength intervals. The simplicity of the method lends itself to the enticing prospect that the method could be applicable to wide-field applications in quantitative fluorescence imaging and dosimetry in photodynamic therapy.
Involvement of a Binuclear Species with the Re−C(O)O−Re Moiety in CO2Reduction Catalyzed by Tricarbonyl Rhenium(I) Complexes with Diimine Ligands:  Strikingly Slow Formation of the Re−Re and Re−C(O)O−Re Species from Re(dmb)(CO)3S (dmb = 4,4‘-Dimethyl-2,2‘-bipyridine, S = Solvent) (2003)

Excited-state properties of fac-[Re(dmb)(CO)(3)(CH(3)CN)]PF(6), [Re(dmb)(CO)(3)](2) (where dmb = 4,4'-dimethyl-2,2'-bipyridine), and other tricarbonyl rhenium(I) complexes were investigated by transient FTIR and UV-vis spectroscopy in CH(3)CN or THF. The one-electron reduced monomer, Re(dmb)(CO)(3)S (S = CH(3)CN or THF), can be prepared either by reductive quenching of the excited states of fac-[Re(dmb)(CO)(3)(CH(3)CN)]PF(6) or by homolysis of [Re(dmb)(CO)(3)](2). In the reduced monomer's ground state, the odd electron resides on the dmb ligand rather than on the metal center. Re(dmb)(CO)(3)S dimerizes slowly in THF, k(d) = 40 +/- 5 M(-1) s(-1). This rate constant is much smaller than those of other organometallic radicals which are typically 10(9) M(-1) s(-1). The slower rate suggests that the equilibrium between the ligand-centered and metal-centered radicals is very unfavorable (K approximately 10(-4)). The reaction of Re(dmb)(CO)(3)S with CO(2) is slow and competes with the dimerization. Photolysis of [Re(dmb)(CO)(3)](2) in the presence of CO(2) produces CO with a 25-50% yield based on [Re]. A CO(2) bridged dimer, (CO)(3)(dmb)Re-CO(O)-Re(dmb)(CO)(3) is identified as an intermediate. Both [Re(dmb)(CO)(3)](2)(OCO(2)) and Re(dmb)(CO)(3)(OC(O)OH) are detected as oxidation products; however, the previously reported formato-rhenium species is not detected.
Evidence implicating phospholipase as a virulence factor of Candida albicans (1995)

Three different approaches were used to investigate the role of extracellular phospholipases in the pathogenicity of Candida albicans. First, we compared 11 blood isolates of this yeast with an equal number of commensal strains isolated from the oral cavities of healthy volunteers. Blood isolates produced significantly more extracellular phospholipase activity than the commensal strains did. Second, two clinical isolates of C. albicans that differed in their levels of virulence in a newborn mouse model were compared for their ability to secrete phospholipases. The invasive strain produced significantly more extracellular phospholipase activity than the noninvasive strain did. Third, nine blood isolates were characterized for their phospholipase and proteinase production, germ tube formation, growth, and adherence to and damage of endothelial cells in vitro. These factors were analyzed subsequently to determine whether they predicted mortality in a mouse model of hematogenously disseminated candidiasis. By proportional hazard analysis, the relative risk of death was 5.6-fold higher (95% confidence interval, 1.672 to 18.84 [P < 0.005]) in the mice infected with the higher-phospholipase-secreting strains than in the low-phospholipase secretors. None of the other putative virulence factors predicted mortality. Characterization of phospholipases secreted by three of the blood isolates showed that these strains secreted both phospholipase B and lysophospholipase-transacylase activities. These results implicate extracellular phospholipase as a virulence factor in the pathogenesis of hematogenous infections caused by C. albicans.
Examining the effect of Withania somnifera supplementation on muscle strength and recovery: a randomized controlled trial (2015)

This study reports that ashwagandha supplementation is associated with significant increases in muscle mass and strength and suggests that ashwagandha supplementation may be useful in conjunction with a resistance training program.
Fluorescence in Mg ix emission at 48.340 Å from Mg pinch plasmas photopumped by Al xromani line radiation at 48.338 Å (1993)

Resonant photopumping of Be-like Mg ix ions by Li-like Al xi line radiation has been studied in pulsed-power-driven plasmas as a possible approach to achieve laser action in the extreme-ultraviolet wavelength region. An Al x-pinch or z-pinch plasma imploded by a 0.5-TW pulsed power generator produced intense line radiation at 48.338 \AA{}. A separate Mg z-pinch plasma, driven by the same pulsed power generator, was created in parallel with 1 cm separating the two plasmas. Evidence for fluorescence (resonant scattering) was the appearance of 48.340-\AA{} resonance line emission from the 4p level of Mg ix ions due to photopumping by the Al xi line radiation at 48.338 \AA{}. Fluorescence may also have been observed on the Mg viii line at 52.395 \AA{}, photopumped by Al xi line radiation at 52.446 \AA{}. Both Al and Mg plasmas were characterized in the experiments. Improvements to the pump geometry required to achieve gain on the Mg ix line at 228 \AA{} are also discussed.
Application of Calcium Phosphate Materials in Dentistry (2013)

Calcium phosphate materials are similar to bone in composition and in having bioactive and osteoconductive properties. Calcium phosphate materials in different forms, as cements, composites, and coatings, are used in many medical and dental applications. This paper reviews the applications of these materials in dentistry. It presents a brief history, dental applications, and methods for improving their mechanical properties. Notable research is highlighted regarding (1) application of calcium phosphate into various fields in dentistry; (2) improving mechanical properties of calcium phosphate; (3) biomimetic process and functionally graded materials. This paper deals with most common types of the calcium phosphate materials such as hydroxyapatite and tricalcium phosphate which are currently used in dental and medical fields.
RecA Protein Filaments Disassemble in the 5′ to 3′ Direction on Single-stranded DNA (2001)

RecA protein forms filaments on both single- and double-stranded DNA. Several studies confirm that filament extension occurs in the 5' to 3' direction on single-stranded DNA. These filaments also disassemble in an end-dependent fashion, and several indirect observations suggest that the disassembly occurs on the end opposite to that at which assembly occurs. By labeling the 5' end of single-stranded DNA with a segment of duplex DNA, we demonstrate unambiguously that RecA filaments disassemble uniquely in the 5' to 3' direction.
Spontaneous Chemical Vapor Growth of NiSi Nanowires and Their Metallic Properties (2007)

A simple and controlled growth of metallic NiSi nanowires at low temperatures (< 400 °C) by a chemical vapor deposition using SiH4 at a low supersaturation limit is reported. It is demonstrated that the simple and low temperature synthesis of metallic nanowires is compatible with conventional Si processing and provide interesting strategies for their possible applications as interconnects in Si microelectronics and as field emitters in field emission displays.