gebhart/patrepeval huggingface dataset:
The complete mitogenomes of the oriental mayfly, Ephemera orientalis (Ephemeroptera: Ephemeridae) and the dragonfly, Davidius lunatus (Odonata: Gomphidae) (2008)

We determined the complete mitogenome of the oriental mayfly, Ephemera orientalis (Ephemeroptera: Ephemeridae) and the dragonfly Davidius lunatus (Odonata: Gomphidae). The 16,463-bp long E. orientalis and the 15,912 bp long D. lunatus mitogenome contains gene arrangement and content identical to the most common type found in a diverse insect order. Most individual E. orientalis and D. lunatus mt genes were well within the size found in the respective genes of other insects. The initiation codon for the D. lunatus COI gene was typical as ATA, whereas no typical start codon was found in the start region of E. orientalis COI gene. The A+T-rich regions of both mitogenomes have a few unusual feature. The A+T-rich region of E. orientalis contains a tandem repeat composed of two identical copies of 55 bp long, whereas that of D. lunatus contains a tandem repeat composed of duplicated identical 261-bp copies and one partial copy of the repeat. Also, the A+T-rich region of E. orientalis contains a single sequence and that of D. lunatus contains nine sequences, along with the tandem triplicate sequences, that has the potential to form stem-and-loop structures, flanked by the conserved sequences, “TA(A)TA” at the 5’ end and “G(A)nT’ at the 3’ end. Furthermore, the A+T-rich region of D. lunatus contains two tRNA-like structures, tRNALeu(UUR)-like sequence and tRNATyr-like sequence that have proper anticodon TAA and clover-leaf structure that were previously found in the hymenopteran insects.
Chiral δ-lactones via Pyranose-annulation (1994)

Abstract The syntheses of chiral δ-lactones 6, 10, 11a,b and 12 from anhydro riboses 1 and 7a,b are described.
Low-Loss Waveguide Bends by Advanced Shape for Photonic Integrated Circuits (2020)

We report the design and experiment of advanced bends which are composed of widening width and varying radius. Advanced bends are based on silicon nitride waveguide for the wavelength of 850 nm and silicon waveguide for the wavelength of 1550 nm. The reduction of bending loss from 0.13 to 0.04 dB/90° by the advanced shape on a silicon nitride waveguide bend with 15 μm-radius at the wavelength of 850 nm was achieved. The bending loss from the silicon advanced bend was measured to be 0.012 dB/90° when R = 2 μm at the wavelength of 1550 nm. This is the best result of 2 μm-bends in a 220 nm-SOI platform at 1550 nm.
Wideband spectrum sensing measurement results using tunable front-end and FPGA implementation (2017)

In this work, we implement a wideband spectrum sensing receiver using Analog Devices AD9361 RF frontend that can be tuned to frequencies from 70MHz to 6GHz with 30.72MHz bandwidth. An energy detection based spectrum sensing algorithm is implemented on Xilinx Kintex-7 FPGA in a pipelined architecture in order to continuously obtain data capture from the RF frontend without any missed samples and reduced latency. The wideband spectrum sensing algorithm uses 8192 FFT bins and provides center frequency and bandwidth of up to 8 non-overlapping frequency bands. The proposed architecture provides frequency resolution of 37.5kHz, time resolution of 8.53ms and latency of 8.78ms.
Energy Crops for the Production of Biofuels (2010)

Numerous options are available to supply biomass to biorefineries. Potential feedstocks include short rotation woody crops, herbaceous energy crops, and residues (forestry and agricultural). Each feedstock has unique chemical and physical properties that will influence the products and profitability from a biorefinery. For example, herbaceous feedstocks will have higher ash contents on average than woody products. Herbaceous feedstocks typically will have a lower lignin content and as a result a lower heating value than woody crops. Feedstock selection should consider the availability of equipment to establish, maintain, and harvest energy crops. In most cases, the equipment required is available to produce energy crops within the forestry and agricultural industries but is not optimized for energy crop production. Deciding which feedstock to produce will depend on site-specific considerations (soil type, temperature, and rainfall) that will influence the cost, yield, and composition of energy crops. Collection, storage, and transportation of energy crops is expensive relative to current fossil fuels, although biomass energy crops have lower greenhouse gas emissions than fossil fuels.
Chordoid glioma: a neoplasm unique to the hypothalamus and anterior third ventricle. (2001)

Chordoid glioma is a recently described unique histopathologic entity that has been added to the World Health Organization glioma classification scheme and must be included in the differential diagnosis of a suprasellar mass. Distinctive imaging features are its location, ovoid shape, hyperdensity on CT scans, and uniform intense contrast enhancement.
Altered signaling at the PTH receptor via modified agonist contacts with the extracellular domain provides a path to prolonged agonism in vivo (2022)

The parathyroid hormone type 1 receptor (PTHR1), a Class B GPCR, is activated by long polypeptides, including drugs for osteoporosis and hypoparathyroidism. The PTHR1 engages peptide agonists via a two-step mechanism. Initial contact involves the extracellular domain (ECD), which has been thought to contribute primarily to receptor-peptide binding, and then the N terminus of the peptide engages the receptor transmembrane domain (TMD), which is thought to control the message conveyed to intracellular partners. This mechanism has been suggested to apply to other Class B GPCRs as well. Here, we show that modification of a PTHR1 agonist at ECD-contact sites can alter the signaling profile, an outcome that is not accommodated by the current two-step binding model. Our data support a modified two-step binding model in which agonist orientation on the ECD surface can influence the geometry of agonist-TMD engagement. This expanded binding model offers a mechanism by which altering ECD-contact residues can affect signaling profile. Our discoveries provide a rationale for exploring agonist modifications distal from the TMD-contact region in future efforts to optimize therapeutic performance of peptide hormone analogs.
Differential effects of cytomegalovirus infection on complement synthesis by human mesangial cells (1997)

Viruses may be eliminated by the host immune system via complement-mediated lysis of infected cells. Previously, we have demonstrated that the synthesis of complement factor B by renal mesangial cells (MC) is enhanced by interferon-alpha (IFN-alpha), -beta and -gamma. In the present study we investigate the effect of human cytomegalovirus (HCMV) infection on the production of complement factors by MC. The production of factor B, C2, C4 and factor H by mock-infected MC was 0.2 +/- 0.4, 3.9 +/- 6.8, 1.7 +/- 0.8 and 149 +/- 36 ng/10(6) cells per 72 h, respectively. In HCMV-infected MC cultures an induction of both factor B and C2 protein synthesis was observed up to 2.2 +/- 1.1 and 156 +/- 74 ng/10(6) cells per 72 h, respectively. The synthesis of C4 and factor H of 2.9 +/- 2.0 and 146 +/- 31 ng/10(6) cells, respectively, was not altered significantly. By Northern blot and reverse transcriptase-polymerase chain reaction (RT-PCR) analysis it was demonstrated that factor B and C2 mRNA expression were up-regulated in HCMV-infected cell cultures, whereas the levels of C4 and factor H mRNA were not changed. When MC cultures were inoculated with heat- or UV-inactivated HCMV no enhancement of factor B mRNA expression was observed. The enhanced expression was not blocked by phosphono acetic acid (PAA), suggesting that expression of the HCMV immediate early or early genes is sufficient to induce complement synthesis. We conclude that infection of MC cultures with HCMV selectively induces complement C2 and factor B production, probably mediated by interferons.
Treatment of murine acute gvhd with the novel pro-apoptotic benzodiazepine Bz-423 (2006)

Bz-423 is a novel 1,4-benzodiazepine with both cytotoxic and cytostatic effects on activated lymphocytes. Bz-423 has been shown to suppress lupus in murine models by eliminating pathogenic lymphocytes without altering normal immune function or overt toxicities. We hypothesized that Bz-423 might enhance the apoptotic deletion of alloreactive donor T cells and therefore reduce graft-versus-host disease (GVHD). We first investigated the effect of Bz-423 on activated T cells in vitro. A 40 μM concentration of Bz-423 induced apoptotic death in >90% of both CD4+ and CD8+ T lymphocytes stimulated with allogeneic dendritic cells (DC) or ConA in the presence of syngeneic DC. Purified resting T cells were significantly less susceptible to Bz-423-induced apoptosis (data not shown). We next examined the effect of Bz-423 in vivo utilizing a well-characterized (Balb/c→B6) murine GVHD model. B6 recipient mice were conditioned with 11 Gy total body irradiation and injected with 5.0 × 106 bone marrow and 4-5.0 × 106 purified T cells from either syngeneic (B6) or allogeneic (Balb/c) donors. In order to model the administration of Bz-423 as a treatment strategy rather than a prevention strategy, animals were not treated for the first seven days after BMT. Beginning 7 days following BMT and continuing for the remainder of the experiment, Bz-423 was administered i.p. at a dose of 60 mg/kg three times weekly. As shown in the table below, treatment with Bz-423 resulted in significantly better day +60 survival (P = .001) and reduced clinical GVHD scores (P < .02) among allogeneic BMT recipients. Bz-423 also reduced GVH-associated immunodeficiency (P = .02) and decreased liver and gut histopathology of GVHD (P = .01). Delay of the onset of treatment to day 14 post-BMT also resulted in a significant survival benefit (P = .03). These data demonstrate that Bz-423 can reverse acute GVHD and induce selective apoptosis of alloreactive donor T cells in this model. Pro-apoptotic benzodiazepines may provide a strategy for the treatment of acute GVHD (Table 1).Tabled 1Syn + BzAllo + vehicleAllo + BzP Value1Calculated at the 95% confidence level, Allo + vehicle vs Allo + Bz-423; 2reported as mean clinical score ± SE; 3reported as mean value ± SD.Treatment onset: day +7 Survival (day 60)100% (n = 9)8% (n = 13)59% (n = 19).001 GVHD clinical score (day 60)21.5 ± 0.26.5 ± 0.03.1 ± 0.4<.02 Pathology (day 74)3 Liver1.3 ± 0.613.7 ± 1.58.3 ± 2.5.01 Intestine3.0 ± 2.021.3 ± 6.010.0 ± 0.8.01 Splenic reconstitution (day 74)3 T cells (×106)20.6 ± 1.81.4 ± 0.023.6 ± 0.4.02 B cells (×106)41.6 ± 12.62.5 ± 0.721.2 ± 15.6.02Treatment onset: day +14 Survival (day 60)100% (n = 3)20% (n = 5)71% (n = 6).031 Calculated at the 95% confidence level, Allo + vehicle vs Allo + Bz-423; 2reported as mean clinical score ± SE; 3reported as mean value ± SD. Open table in a new tab
Abstract 14505: An Early Transcriptomic Signature Predicts Poor Outcome After Out-of-hospital Cardiac Arrest (2017)

Introduction: Early prognostication is a major challenge in comatose survivors of OHCA. Hypothesis: We hypothesized that a wide analysis of the transcriptome could offer new prognostic tools and research axes. Methods: Patients were enrolled from an ancillary study of the clinical trial NCT00999583 that tested the effect of a high dose of erythropoietin (EPO) after OHCA. Blood samples were collected in comatose survivors of cardiac arrest at hospital admission and at days 1 and 3. Whole-blood RNA was purified, and processed to be hybridized on an Illumina HumanHT-12 V4 gene expression BeadChip, allowing a follow up of more than 34000 genes. Transcriptome profiles were compared between patients with favorable vs poor outcome (Cerebral performance category [CPC] 1-2 vs CPC>2) and treated or not by EPO (fold change >1.3; p<0.05). Results: Blood collection was performed in 69 patients. Among them, 33 and 36 patients were treated by EPO or not, respectively. The outcome was not different between these two grou...
Noninvasive k3 estimation method for slow dissociation PET ligands: application to [11C]Pittsburgh compound B (2013)

In [11C]PIB, the applicability of 3P++ analysis may be restricted to intra-subject comparison such as follow-up studies. The 3P++ method itself is thought to be robust and may be more applicable to other non-highly reversible PET ligands with ideal reference tissue.
Characterizing the effects of silver alloying in chalcopyrite CIGS solar cells with junction capacitance methods (2009)

A variety of junction capacitance-based characterization methods were used to investigate alloys of Ag into Cu(In1-xGax)Se2 photovoltaic solar cells over a broad range of compositions. These alloys show encouraging trends of increasing VOC with increasing Ag content, opening the possibility of wide-gap cells for use in tandem device applications. Drive level capacitance profiling (DLCP) has shown very low free carrier concentrations for all Ag-alloyed devices, in some cases less than 1014 cm-3, which is roughly an order of magnitude lower than that of CIGS devices. Transient photocapacitance spectroscopy has revealed very steep Urbach edges, with energies between 10 meV and 20 meV, in the Ag-alloyed samples. This is in general lower than the Urbach edges measured for standard CIGS samples and suggests a significantly lower degree of structural disorder.
Improved single-mode emission characteristics of long-wavelength wafer-fused vertical-cavity surface-emitting lasers by intra-cavity patterning (2013)

We report on transverse mode discrimination in long-wavelength wafer-fused vertical-cavity surface-emitting lasers (VCSELs) incorporating ring-shaped air gap patterns at the fused interface between the active region and the top distributed Bragg reflector (DBR). These 60-nm deep patterns were implemented with the aim of favoring the fundamental mode while preserving high output power. The VCSELs under consideration emit in the 1310-nm band and incorporate an AlGaInAs-based quantum well active region, a regrown circular tunnel junction and undoped GaAs/AlGaAs DBRs. A large batch of devices with varying pattern dimensions was investigated by on-wafer mapping, allowing significant statistical analysis leading to conclusions on their typical behavior. We observe experimentally a dependence of the side-mode suppression ratio on the geometrical parameters of the patterns. In particular, we identified a design that statistically increases the maximal single-mode emitted power by more than 20%. Numerical simulations of the patterned-cavity VCSELs based on our fully three dimensional electrical, thermal and optical VCSEL computational model support these observations. They show that patterns with a large inner diameter actually confine the first-order transverse mode and enhance its modal gain. In smaller devices, this mode is pushed out of the optical aperture and suffers larger losses. Optimized parameters were found numerically for enhancing the single-mode properties of the devices with negligible penalty on emitted power and threshold current.
NMI Linkage Modification Increases Potency and Stability of H-RASAntisense Oligonucleotides (1999)

Abstract Phosphorothioate antisense oligodeoxyribonucleotides (PS-ASOs) have proven to be useful first generation antisense tools for in vitro and in vivo uses and now show great promise as human therapeutic agents. However, there are two characteristics of PS-ASOs that make it desirable to continue to attempt to improve their biophysical characteristics through chemical modification. First, PS-ASOs have been reported, at very high concentrations, to have some nonspecific activities, both in vitro and in vivo, usually attributed to their protein binding properties. Second, while significantly more stable than their phosphodiester analogues, the in vivo stability of phosphorothioate oligonucleotides can still be improved. This instability is primarily due to 3′ exonucleases, 5′ exonucleases, and to a lesser degree, endonucleases. There is a strong rationale for exploring backbone modifications that can reduce the P=S content and maintain or increase nuclease resistance of antisense oligonucleotides. One such modification, methylene(methyl)imino (MMI), allows for complete substitution of the phosphate backbone while maintaining high affinity for the target RNA and enhanced nuclease resistance.1,2 This modification is incorporated into the oligonucleotide as MMI-dimers.
TOXICOLOGY OF METAM SODIUM (2001)

Metam sodium is the third most commonly used agricultural pesticide (by weight) in the U.S. A spill of 19,000 gallons of metam sodium into the Sacramento River in 1991 clearly demonstrated that a major uncontrolled release can have adverse ecological and human health effects. Furthermore, this incident revealed that estimates of Reference Exposure Levels for the major breakdown product of metam sodium (methylisothiocyanate, MITC) were reasonable with regard to the induction of discomfort. In fact, the irritant properties of MITC seem to account for many of the most commonly reported symptoms in this incident. However, neurotoxicity may also account for some of these symptoms. There is evidence that metam sodium can act as a contact sensitizer in humans, inducing allergic dermatitis. It also may exacerbate or induce respiratory allergy (asthma). The ecological impact of routine use of metam sodium is not clear, but adverse effects on non-target plants have been inferred from modeling studies, and adverse effects on soil microbes have been observed. These issues deserve further study. Human health effects of occupational or routine environmental exposure to metam sodium are not known, but there is limited evidence for immunological (hypersensitivity) and developmental effects as well as irritation and associated symptoms. Animal studies suggest a potential for immunological, developmental, carcinogenic, and atherogenic effects. Metam sodium and some of its breakdown products have a wide variety of molecular and cellular actions that could explain the health effects noted here. However, further studies are needed to relate specific molecular or cellular actions to specific health effects.
Bile Duct Reconstruction by a Young Surgeon in Living Donor Liver Transplantation Using Right Liver Graft (2014)

Biliary strictures and bile leaks account for the majority of biliary complications after living donor liver transplantation (LDLT). The aim of this study was to examine differences in biliary complications after adult LDLTs were performed by an experienced senior surgeon and an inexperienced junior surgeon. Surgeries included bile duct reconstruction after adult LDLT using a right liver graft, and risk factors for biliary stricture were identified. We retrospectively reviewed the medical records of 136 patients who underwent LDLT in order to identify patients who developed biliary complications. The senior surgeon performed 102 surgeries and the junior surgeon performed 34 surgeries. The proportion of patients with biliary stricture was similar between the senior and the junior surgeons (27.5% vs 26.5%; P = 0.911). However, the incidence of biliary leakage was higher in patients of the junior surgeon than in those of the senior surgeon (23.5% vs 2.9%; P = 0.001). The frequency of percutaneous drainage was also higher for the junior surgeon than the senior surgeon because of the junior surgeon's high leakage rate of the drainage. When the junior surgeon performed bile duct anastomosis, biliary leakage occurred in 7 patients between the 11th and 20th cases. However, biliary leakage occurred in only 1 case thereafter. Bile duct reconstruction performed by beginner surgeons in LDLT using right lobe grafts should be cautiously monitored and observed by a senior surgeon until an inexperienced junior surgeon has performed at least 20 cases, because of the high incidence of biliary leakage related to surgeon's inexperience in bile duct reconstructions in LDLT.
Novel approach to the synthesis of 6-[F-18]-fluoro-(meta)-tyrosine and related [F-18]-fluorocatecholamines (2000)

There are an estimated 1–2 million victims of Parkinson's disease (PD) in the United States today. Two 18F-labeled tyrosine derivatives, 6-fluoro-DOPA (FDOPA) and 6-fluoro-meta-tyrosine (FMT), have been demonstrated to be useful PET (positron emission tomography) radiopharmaceuticals for the diagnosis and study of PD and related movement disorders in humans. However, existing electrophilic and nucleophilic radiosynthetic approaches to these agents have drawbacks, which make it difficult for most cyclotron-PET facilities to prepare FDOPA or FMT for routine clinical diagnostic applications. This work explored a novel two-step, no-carrier-added, nucleophilic labeling approach to [18F]FMT that may also be applicable to FDOPA and other 18F-fluorocatecholamines. The basic strategy was developed through chemical and radiochemical studies on model compounds. Aromatic nucleophilic [18F]fluoride labeling of a benzophenone precursor containing a 3,5-(bis)trifluoromethylbenzoyl (BTFB) “latent phenol” function on a phenyl substituted with leaving groups (nitro or trimethylammonium), followed by “unmasking” the BTFB function by Baeyer-Villiger oxidation gave [18F]fluorophenols rapidly and in good radiochemical yields. Catalytic enantioselective alkylation was used to attach the protected amino acid (AA) side-chain to the benzophenone moiety and construct the homochiral FMT labeling precursor. Important radiosynthetic intermediates in unlabeled (19F) form were synthesized independently. The Baeyer-Villiger reaction was optimized so that the latent phenol and AA protecting groups could be unmasked quickly and efficiently without over-oxidation of the aromatic ring or destruction of the AA side-chain. The optimization process was conducted on a 1–3 mg scale using authentic intermediates in unlabeled form. Products were verified by HPLC and high-resolution mass spectrometry. Optimization of the radiofluorination step is ongoing. The AA side-chain protecting group in the first precursor candidate interfered with labeling, apparently by forming covalent 18F-adducts involving the hexafluoroacetonide protecting group instead of the aromatic ring. Other AA protecting groups are being evaluated to overcome this difficulty. It is anticipated that minor modifications of this general route will provide a straightforward, practical synthesis of [18F]FMT and related PET agents.
Tin monosulfide thin films grown by atomic layer deposition using tin 2,4 pentandionate and hydrogen sulfide (2010)

Tin monosulfide (SnS) was grown by atomic layer deposition (ALD) using sequential exposures of tin(II) 2,4- pentanedionate (Sn(acac)<sup>2</sup>) and hydrogen sulfide (H2S). In situ quartz crystal microbalance (QCM) studies showed that the SnS ALD mass gain per cycle was 11-12 ng/cm<sup>2</sup> at 175°C on a gold-covered QCM sensor. Using a film density of 5.07 g/cm3 determined by X-ray reflectivity measurements, these mass gains are equivalent to SnS ALD growth rates of 0.22-0.24 &Aring;/cycle. The ratio of the mass loss and mass gain ratio |&utri;m<sup>2</sup>/&utri;m1| from the H2S and Sn(acac)<sub>2</sub> reactions was |&utri;m<sup>2</sup>/&utri;m1| ~0.32 at 175 °C. This measured ratio is close to the predicted ratio from the proposed surface chemistry for SnS ALD. The SnS ALD was self-limiting versus the Sn(acac)2 and H2S exposures. The SnS ALD growth rate was also independent of substrate temperature from 125-225 °C. X-ray fluorescence studies confirmed a Sn/S atomic ratio of ~1.0 for the SnS ALD films. X-ray photoelectron spectroscopy measurements revealed that the SnS ALD films contained oxygen impurities at 15-20 at% after air exposure. These oxygen-containing SnS ALD films displayed a bandgap of ~1.87 eV that is higher than the SnS bulk value of ~1.3 eV.