gebhart/patrepeval huggingface dataset:
Polyglycine hydrolases: Fungal β‐lactamase‐like endoproteases that cleave polyglycine regions within plant class IV chitinases (2015)

Polyglycine hydrolases are secreted fungal proteases that cleave glycine-glycine peptide bonds in the inter-domain linker region of specific plant defense chitinases. Previously, we reported the catalytic activity of polyglycine hydrolases from the phytopathogens Epicoccum sorghi (Es-cmp) and Cochliobolus carbonum (Bz-cmp). Here we report the identity of their encoding genes and the primary amino acid sequences of the proteins responsible for these activities. Peptides from a tryptic digest of Es-cmp were analyzed by LC-MS/MS and the spectra obtained were matched to a draft genome sequence of E. sorghi. From this analysis, a 642 amino acid protein containing a predicted β-lactamase catalytic region of 280 amino acids was identified. Heterologous strains of the yeast Pichia pastoris were created to express this protein and its homolog from C. carbonum from their cDNAs. Both strains produced recombinant proteins with polyglycine hydrolase activity as shown by SDS-PAGE and MALDI-MS based assays. Site directed mutagenesis was used to mutate the predicted catalytic serine of Es-cmp to glycine, resulting in loss of catalytic activity. BLAST searching of publicly available fungal genomes identified full-length homologous proteins in 11 other fungi of the class Dothideomycetes, and in three fungi of the related class Sordariomycetes while significant BLAST hits extended into the phylum Basidiomycota. Multiple sequence alignment led to the identification of a network of seven conserved tryptophans that surround the β-lactamase-like region. This is the first report of a predicted β-lactamase that is an endoprotease.
Direct generation of 20 W peak power picosecond optical pulses from an external-cavity mode-locked GaInN laser diode incorporating a flared waveguide (2011)

We directly generated 1.6-ps optical pulses with a peak power of 20 W at a repetition of 1 GHz using a blue-violet GaInN mode-locked laser diode incorporating a flared waveguide operating in single transverse mode. The flared waveguide enabled optical pulses to be generated with peak powers of over six times higher than those produced using a straight waveguide while preserving the pulse duration.
Supplementary File 3 from Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays (2023)

Supplementary File 3 from Identifying Allelic Loss and Homozygous Deletions in Pancreatic Cancer without Matched Normals Using High-Density Single-Nucleotide Polymorphism Arrays
Supplementary Table 1 from c-Src Modulates Estrogen-Induced Stress and Apoptosis in Estrogen-Deprived Breast Cancer Cells (2023)

&lt;p&gt;PDF file - 59K, Sequences of Primers.&lt;/p&gt;
Control of Ga-oxide interlayer growth and Ga diffusion in SiO2/GaN stacks for high-quality GaN-based metal–oxide–semiconductor devices with improved gate dielectric reliability (2017)

A simple and feasible method for fabricating high-quality and highly reliable GaN-based metal–oxide–semiconductor (MOS) devices was developed. The direct chemical vapor deposition of SiO2 films on GaN substrates forming Ga-oxide interlayers was carried out to fabricate SiO2/GaOx/GaN stacked structures. Although well-behaved hysteresis-free GaN-MOS capacitors with extremely low interface state densities below 1010 cm−2 eV−1 were obtained by postdeposition annealing, Ga diffusion into overlying SiO2 layers severely degraded the dielectric breakdown characteristics. However, this problem was found to be solved by rapid thermal processing, leading to the superior performance of the GaN-MOS devices in terms of interface quality, insulating property, and gate dielectric reliability.
Population Intervention Causal Effects Based on Stochastic Interventions (2011)

Estimating the causal effect of an intervention on a population typically involves defining parameters in a nonparametric structural equation model (Pearl, 2000, Causality: Models, Reasoning, and Inference) in which the treatment or exposure is deterministically assigned in a static or dynamic way. We define a new causal parameter that takes into account the fact that intervention policies can result in stochastically assigned exposures. The statistical parameter that identifies the causal parameter of interest is established. Inverse probability of treatment weighting (IPTW), augmented IPTW (A-IPTW), and targeted maximum likelihood estimators (TMLE) are developed. A simulation study is performed to demonstrate the properties of these estimators, which include the double robustness of the A-IPTW and the TMLE. An application example using physical activity data is presented.
A Facile Entry into Naphthopyran Quinones via an Annelation Reaction of Levoglucosenone. The Total Synthesis of (−)-Hongconin1 (1996)

The annelation reactions of levoglucosenone, prepared by pyrolysis of paper, with 3-cyano-1(3H)-isobenzofuranone and 3-cyano-5-methoxy-1(3H)-isobenzofuranone have been studied. Reductive ring-opening of the annelation products with zinc/copper couple and subsequent chemical transformations provide a facile entry into the naphthopyran quinone ring system. Standard chemical transformations of the annelation product from 3-cyano-5-methoxy-1(3H)-isobenzofuranone and levoglucosenone afforded (1R)-5,9,10-trimethoxy-1-methyl-1H-naphtho[2,3-c]pyran-4(3H)-one. The lithium enolate of this compound undergoes an interesting and potentially useful reaction with oxygen to afford (3R)-4,5,9-trimethoxy-3-methylnaphtho[2,3-c]furan-1(3H)-one. When oxygen is rigorously excluded, methylation of the enolate could be performed in good yield using 10 equiv of methyl iodide in the presence of 10 equiv of DMPU. This chemistry culminated in a total synthesis of (-)-hongconin in six steps from levoglucosenone.
Saturable transport of insulin from plasma into the central nervous system of dogs in vivo. A mechanism for regulated insulin delivery to the brain. (1993)

By acting in the central nervous system, circulating insulin may regulate food intake and body weight. We have previously shown that the kinetics of insulin uptake from plasma into cerebrospinal fluid (CSF) can best be explained by passage through an intermediate compartment. To determine if transport kinetics into this compartment were consistent with an insulin receptor-mediated transport process, we subjected overnight fasted, anesthetized dogs to euglycemic intravenous insulin infusions for 90 min over a wide range of plasma insulin levels (69-5,064 microU/ml) (n = 10). Plasma and CSF samples were collected over 8 h for determination of immunoreactive insulin levels, and the kinetics of insulin uptake from plasma into CSF were analyzed using a compartmental model with three components (plasma-->intermediate compartment-->CSF). By sampling frequently during rapid changes of plasma and CSF insulin levels, we were able to precisely estimate three parameters (average standard deviation 14%) characterizing the uptake of insulin from plasma, through the intermediate compartment and into CSF (k1k2); insulin entry into CSF and insulin clearance from the intermediate compartment (k2 + k3); and insulin clearance from CSF (k4). At physiologic plasma insulin levels (80 +/- 7.4 microU/ml), k1k2 was determined to be 10.7 x 10(-6) +/- 1.3 x 10(-6) min-2. With increasing plasma levels, however, k1k2 decreased progressively, being reduced sevenfold at supraphysiologic levels (5,064 microU/ml). The apparent KM of this saturation curve was 742 microU/ml (approximately 5 nM). In contrast, the rate constants for insulin removal from the intermediate compartment and from CSF did not vary with plasma insulin (k2 + k3 = 0.011 +/- 0.0019 min-1 and k4 = 0.046 +/- 0.021 min-1). We conclude that delivery of plasma insulin into the central nervous system is saturable, and is likely facilitated by an insulin-receptor mediated transport process.
Transplantation: Immunogenetic and Clinical Aspects—Part I (1982)

Although graft survival has not really improved overall in the past decade, we may be at a turning point in the history of transplantation, armed with new information about the immunogenetics of rejection and new modes of therapy. The use of multiple blood transfusions to precondition potential recipients toward acceptance has had a major impact on enhancement of organ survival.
Internal Quantum Efficiency of Nitride-based Light-Emitting Diodes (2008)

The internal quantum efficiency (IQE) of InGaN-based light-emitting diodes has been studied by means of excitation-power-density- and temperature-dependent photoluminescence spectroscopy. The IQE was evaluated at various excitation photon energies using a wavelength-tunable dye laser system. The IQE obtained under selective excitation of InGaN active layers was higher than that obtained under band-to-band excitation of GaN and AlGaN cladding layers. The enhanced value of IQE under selective excitation reflected the intrinsic optical quality of the InGaN active layer itself.
Enhanced photoelectrochemical performance of bridged ZnO nanorod arrays grown on V-grooved structure (2012)

Bridged ZnO nanorod arrays on a V-grooved Si(100) substrate were used as the photoanode of a photoelectrochemical (PEC) cell for water splitting. Photolithography followed by reactive ion etching was employed to create a V-grooved structure on a Si substrate. ZnO nanorod arrays were grown via a hydrothermal method. The light trapping and PEC properties are greatly enhanced using the bridged ZnO nanorod arrays on a V-grooved Si substrate compared with those on a flat one. Increased short circuit photocurrent density (JSC, 0.73 mA cm−2) and half-life time (1500 s) are achieved. This improved JSC and half-life time are 4 times and 10 times, respectively, higher than those of the ZnO nanorod arrays grown on a flat substrate. The overall PEC cell performance improvement for the V-groove grown ZnO array is attributed to the reduced light reflection and enhanced light trapping effect. Moreover, V-groove ZnO showed stronger adhesion between ZnO nanorod arrays and the substrate.
P1-03-08: Adipose Tissue in Breast Cancer: Not an Idle Bystander but an Active Participant in Breast Cancer Progression. (2011)

Abstract Background: Adipose tissue is a dynamic organ that secretes a plethora of molecules called adipokines. In breast cancer we find a unique situation were genetically changed cells (the cancer cells) are in close contact with adipocytes. Moreover, obesity is a known negative prognostic marker for postmenopausal breast cancer patients. We hypothesize that adipocyte-derived factors influence breast cancer progression. Materials and methods: Adipose tissue was collected from breast cancer patients undergoing a mastectomy. After macroscopic removal of blood vessels and connective tissue, the adipose tissue was carefully cut into 2–3mm3 pieces and were incubated in specific adipose-tissue culture medium. After 24h, the medium was collected and the quality was checked by determining the concentration of total proteins, leptin, adiponectin, TNFalpha and triglycerides. This conditioned medium of adipose tissue (CM AT) was used for in vitro experimentation with MCF-7 breast cancer cells. Results: Effect of AT on morphology and aggregation: when MCF-7 cells are grown in a culture flask, they tend to form round compact islands. Under influence of CM AT, the islands form sharp edges, the cells in an island can be counted individually and they show scattering. Importantly, despite the major changes in cellular morphology, CM AT removal rescued the compact island formation of MCF-7 cells. In the slow aggregation assay, cells treated with CM AT (and a subtherapeutic concentration of a neutralizing E-cadherin antibody) lost the ability to form compact aggregates. Furthermore, MCF-7 spheroids placed inside adipose tissue showed massive reorganization into an irregularly shaped mass. Effect of AT on proliferation: starting from an equal number of cells and counting them every 2 days, it became clear that MCF-7 cells with CM AT had a higher rate of proliferation than MCF-7 cells in control medium. This stimulation of proliferation was confirmed by cell cycle analysis which revealed a doubling of cells in the G2/M phase, and western blot which showed an upregulation of cyclin A and cyclin E, both positive regulators of the cell cycle. Effect of AT on invasion: a 24h collagen type I invasion assay revealed invasive characteristics of MCF-7 cells treated with CM AT while MCF-7 cells in control conditions are round and non-invasive. In contrast, a transwell collagen test over 14 days was not able to show MCF-7 cells invading the collagen gel under influence of CM AT. However, the growth pattern of MCF-7 cells on the collagen gel was clearly disorganised when compared with the control situation. Conclusion: These findings suggest that adipose tissue-derived factors exert a dramatic selective force on patterning, invasion and growth of MCF-7 breast cancer cells. Unraveling the mechanism behind these observations may provide vital information regarding the link between obesity and poor prognosis in postmenopausal breast cancer. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-03-08.
Fatal Stent-Associated Respiratory Tract Infection Caused by K64-ST11 KPC-2-Producing Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae : A Rare Case Report (2023)

<b><i>Objectives:</i></b> This study reported a fatal stent-associated respiratory tract infection (SARTI) caused by carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> (CR-hvKP). <b><i>Case:</i></b> A bare-metal stent in the left main bronchus and a Y-shaped stent graft in the tracheal bronchus were placed successively in a 50-year-old woman due to shortness of breath after undergoing multiple chemotherapy treatments for lung cancer. Unfortunately, the followed SARTI and lung abscess in our patient caused by CR-hvKP eventually led to the death of the patient, despite our aggressive clearing of phlegm and potent antibiotics. The genomic analysis showed it was caused by a KPC-2-producing extensively drug-resistant K64-ST11 hypervirulent <i>K. pneumoniae</i> harboring several virulence and antimicrobial resistance genes. <b><i>Conclusion:</i></b> This study highlights the risk of SARTI caused by CR-hvKP in immunocompromised individuals.
Fast 31P chemical shift imaging using SSFP methods (2002)

Steady-state free precession (SSFP) methods have been very successful due to their high signal and short imaging times. These properties make them good candidates for applications that intrinsically suffer from low signal such as low gamma nuclei imaging. A new chemical shift imaging (CSI) technique based on the SSFP signal formation has been implemented and applied to (31)P. The signal properties of the SSFP CSI method have been evaluated and the steady-state signal of (31)P has been measured in human muscles. Due to the T(2) and T(1) signal dependence of SSFP, the steady-state signal mainly consists of phosphocreatine (PCr). The technique allows fast CSI acquisitions with high SNR of the PCr signal. The SNR gain for PCr over a FLASH-based CSI method is approx. 4-5. Fast in vivo CSI of human muscle with subcentimeter resolution and high SNR is demonstrated at 2 T.
Data from G-Quadruplexes Induce Apoptosis in Tumor Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Several G-rich oligodeoxynucleotides (ODNs), which are capable of forming G-quadruplexes, have been shown to exhibit antiproliferative activity against tumor cell lines and antitumor activity in nude mice carrying prostate and breast tumor xenografts. However, the molecular basis for their antitumor activity remains unclear. In the current study, we showed that a variety of telomeric G-tail oligodeoxynucleotides (TG-ODNs) exhibited antiproliferative activity against many tumor cells in culture. Systematic mutational analysis of the TG-ODNs suggests that the antiproliferative activity depends on the G-quadruplex conformation of these TG-ODNs. TG-ODNs were also shown to induce poly(ADP-ribose) polymerase-1 cleavage, phosphatidylserine flipping, and caspase activation, indicative of induction of apoptosis. TG-ODN–induced apoptosis was largely ataxia telangiectasia mutated (ATM) dependent. Furthermore, TG-ODN–induced apoptosis was inhibited by the c-Jun NH&lt;sub&gt;2&lt;/sub&gt;-terminal kinase (JNK) inhibitor SP600125. Indeed, TG-ODNs were shown to activate the JNK pathway in an ATM-dependent manner as evidenced by elevated phosphorylation of JNK and c-Jun. Interestingly, a number of G-quadruplex ODNs (GQ-ODN) derived from nontelomeric sequences also induced ATM/JNK-dependent apoptosis, suggesting a possible common mechanism of tumor cell killing by GQ-ODNs. (Cancer Res 2006; 66(24): 11808-16)&lt;/p&gt;&lt;/div&gt;
Rigorous Comparison of Gravimetry Employing Atom Interferometers and the Measurement of Gravitational Time Dilation (2011)

We present a gravitationally rigorous and clear answer, in the negative, to the question whether gravimetry with atom interferometers is equivalent to the the measurement of the relative gravitational time dilation of two clocks separated in space. Though matter and light waves, quantum states and oscillator clocks are quantum synonymous through the Planck-Einstein-de Broglie relations and the equivalence principle, there are crucial differences in the context of tests of gravitation theories.
A Phase I Study of Topotecan, Carboplatin and the PARP Inhibitor Veliparib in Acute Leukemias, Aggressive Myeloproliferative Neoplasms, and Chronic Myelomonocytic Leukemia (2016)

<b>Purpose:</b> The PARP inhibitor veliparib delays DNA repair and potentiates cytotoxicity of multiple classes of chemotherapy drugs, including topoisomerase I inhibitors and platinating agents. This study evaluated veliparib incorporation into leukemia induction therapy using a previously described topotecan/carboplatin backbone.<b>Experimental Design:</b> Employing a 3+3 trial design, we administered escalating doses of veliparib combined with topotecan + carboplatin in relapsed or refractory acute leukemias, aggressive myeloproliferative neoplasms (MPN), and chronic myelomonocytic leukemia (CMML).<b>Results:</b> A total of 99 patients received veliparib 10-100 mg orally twice daily on days 1-8, 1-14, or 1-21 along with continuous infusion topotecan 1.0-1.2 mg/m<sup>2</sup>/d + carboplatin 120-150 mg/m<sup>2</sup>/d on days 3-7. The MTD was veliparib 80 mg twice daily for up to 21 days with topotecan 1.2 mg/m<sup>2</sup>/d + carboplatin 150 mg/m<sup>2</sup>/d. Mucositis was dose limiting and correlated with high veliparib concentrations. The response rate was 33% overall (33/99: 14 CR, 11 CRi, 8 PR) but was 64% (14/22) for patients with antecedent or associated aggressive MPNs or CMML. Leukemias with baseline DNA repair defects, as evidenced by impaired DNA damage-induced FANCD2 monoubiquitination, had improved survival [HR = 0.56 (95% confidence interval, 0.27-0.92)]. A single 80-mg dose of veliparib, as well as veliparib in combination with topotecan + carboplatin, induced DNA damage as manifested by histone H2AX phosphorylation in CD34<sup>+</sup> leukemia cells, with greater phosphorylation in cells from responders.<b>Conclusions:</b> The veliparib/topotecan/carboplatin combination warrants further investigation, particularly in patients with aggressive MPNs, CMML, and MPN- or CMML-related acute leukemias. <i>Clin Cancer Res; 23(4); 899-907. ©2016 AACR</i>.
Role of Backbone Chemistry and Monomer Sequence in Amphiphilic Oligopeptide- and Oligopeptoid-Functionalized PDMS- and PEO-Based Block Copolymers for Marine Antifouling and Fouling Release Coatings (2017)

Poly(dimethylsiloxane) (PDMS)- and poly(ethylene oxide) (PEO)-based block copolymer coatings functionalized with amphiphilic, surface-active, and sequence-controlled oligomer side chains were studied to directly compare the effects of hydrophilicity, hydrogen bonding, and monomer sequence on antifouling performance. Utilizing a modular coating architecture, structurally similar copolymers were used to make direct and meaningful comparisons. Amphiphilic character was imparted with non-natural oligopeptide and oligopeptoid pendant chains made from oligo-PEO and surface-segregating fluoroalkyl monomer units. Surface analysis revealed rearrangement for all surfaces when moved from vacuum to wet environments. X-ray photoelectron spectroscopy (XPS) spectra indicated that the polymer backbone and oligomer interactions play key roles in the surface presentation. Biofouling assays using the macroalga Ulva linza showed that the presence of peptoid side chains facilitated the removal of sporelings from the PDMS block copolymer, with removal matching that of a PDMS elastomer standard. The lack of a hydrogen bond donor in the peptoid backbone likely contributed to the lower adhesion strength of sporelings to these surfaces. Both the initial attachment and adhesion strength of the diatom Navicula incerta were lower on the coatings based on PEO than on those based on PDMS. On the PEO coating bearing the blocky peptoid sequence, initial attachment of N. incerta showed no measurable cell density.
Japanese pitch conversion for voice morphing based on differential modeling (2009)

Abstract In this paper, we convert the pitch contours predicted by a TTSsystem that models a source speaker to resemble the pitch con-toursofatargetspeaker. Whenthespeakingstylesofthespeak-ers are very different, complex conversions such as adding ordeletingpitchpeaksmayberequired. Ourmethoddoesthecon-versions by modeling the direct pitch features and differentialpitch features at the same time based on linguistic features. Thedifferential pitch features are calculated from matched pairs ofsource and target pitch values. We show experimental results inwhich the target speaker’s characteristics are successfully mod-eledbasedonaverylimitedtrainingcorpus. TheproposedpitchconversionmethodstretchesthepossibilitiesofTTScustomiza-tion for various speaking styles. Index Terms : pitch conversion, voice conversion, voice mor-phing, speech synthesis, differential modeling. 1. Introduction Voice conversion changes the characteristics of the voice of anSPS (SPeaker Source) to those of an SPT (SPeaker Target) forvarious applications. One important application is to build cus-tomized text-to-speech (TTS) systems for different companies,soaTTSsystemwitheachcompany’sfavoritevoicecanbecre-ated quickly and inexpensively by modifying the speech corpusof some original speaker.Spectra and prosody are the two major characteristics ofvoice. For spectral conversion, recent work such as [1, 2]has achieved signiﬁcant improvements in the naturalness andsimilarity of the voices converted using only a limited amountof training data. However, not much research has been doneinto prosody conversion. Most spectral conversion researchuses simple linear transformations for the prosody. It is truethat the detailed prosody difference is sometimes difﬁcult forlisteners to distinguish [3], especially when the speakers aremonotonously reading for TTS corpus recording. However, togenerate TTS voices with a lively colloquial speaking style, re-production of the detailed prosody characteristics is important.Our objective is to reproduce the SPT’s speaking style ofpitch contours based on limited training data. We assume 100sentences as training data is a reasonable amount to require forthe SPT’s speech corpus. A speech corpus with that size caneasily be recorded in a thirty-minute recording session. We donot assume the existence of a parallel corpus, which can be adifﬁcult condition to satisfy. We focus on the pitch changesaround the syllable level, because the important pitch changesin Japanese are mainly at the syllable level.Figure 1 illustrates examples of pitch contour pairs that theproposed pitch conversion method can handle. They are (a)asymmetrical slope changes, (b) adding or deleting peaks, and(c) adding or deleting phrase-ﬁnal rises.