gebhart/patrepeval huggingface dataset:
Mode of Action for Linear Peptide Inhibitors of HIV-1 gp120 Interactions (2004)

The linear peptide 12p1 (RINNIPWSEAMM) was previously isolated from a phage display library and was found to inhibit interaction of HIV-1 gp120 with both CD4 and a CCR5 surrogate, mAb 17b [Ferrer, M., and Harrison, S. (1999) J. Virol. 73, 5795-5802]. In this work, we investigated the mechanism that leads to this dual inhibition of gp120 binding. We found that there is a direct interaction of 12p1 with gp120, which occurs with a binding stoichiometry of 1:1. The peptide inhibits binding of monomeric YU2 gp120 to both sCD4 and 17b at IC(50) values of 1.1 and 1.6 microM, respectively. The 12p1 peptide also inhibited the binding of these ligands to trimeric envelope glycoproteins, blocked the binding of gp120 to the native coreceptor CCR5, and specifically inhibited HIV-1 infection of target cells in vitro. Analyses of sCD4 saturation of monomeric gp120 in the presence or absence of a fixed concentration of peptide suggest that 12p1 suppression of CD4 binding to gp120 is due to allosteric inhibitory effects rather than competitive inhibition of CD4 binding. Using a panel of gp120 mutants that exhibit weakened inhibition by 12p1, the putative binding site of the peptide was mapped to a region immediately adjacent to, but distinguishable from, the CD4 binding footprint. In the case of the peptide, the effects of single-12p1 residue substitutions and various peptide truncations indicate that the side chain of Trp7 and other structural elements of 12p1 are critical for gp120 binding or efficient inhibition of binding of a ligand to gp120. Finally, 12p1 was unable to inhibit binding of sCD4 to a gp120 mutant that is believed to resemble the CD4-induced conformation of gp120. These results suggest that 12p1 preferentially binds gp120 prior to engagement of CD4; binding of the peptide to gp120 limits the interaction with ligands (CD4 and CCR5) that are generally crucial for viral entry. More importantly, these results indicate that 12p1 binds to a unique site that may prove to be a prototypic target for novel CD4-gp120 inhibitors.
Human neuropeptide Y potentiates α1-adrenergic blood pressure responses in vivo (1998)

Human neuropeptide Y (hNPY) potentiates the postjunctional vasoconstrictor effects of alpha1-adrenoceptor agonists in animals and in human hand veins in vivo. We therefore hypothesized that such an interaction might also occur in the human arterial bed. With the present single-blind cross-over study in 12 healthy volunteers, the effect of subpressor doses of hNPY on the blood pressure response to alpha1-adrenoceptor stimulation was evaluated. Dose-response curves were constructed to intravenously infuse phenylephrine with and without coinfusion with two different doses of hNPY (1.4 and 14.3 pmol . kg-1 . min-1). Blood pressure, heart rate, and forearm blood flow were recorded, and plasma hNPY was determined. During infusion of the higher hNPY dose, which increased hNPY from 24.0 +/- 12.0 to 495.1 +/- 12.6 pmol/l, blood pressure curves were 2.4-fold shifted toward lower phenylephrine dose rates (P < 0.001). Forearm vascular resistance showed a similar trend, whereas the counterregulatory decrease of heart rate was similar in both groups. In contrast, the lower hNPY dose rate producing a fourfold increase in hNPY concentrations did not modify the response to phenylephrine. This in vivo study in humans demonstrates that hNPY induced potentiating effects on alpha1-adrenergic constriction also in the systemic arterial circulation and suggests that circulating hNPY may participate in the control of vascular tone.
Acute and Chronic Renal Failure in Liver Transplantation (1990)

We have performed a retrospective review of the incidence and etiologies of acute renal failure (ARF) in 105 adult patients receiving liver transplants. The prevalence of chronic renal failure was also determined. ARF occurred in 94.2% of these patients. Acute tubular necrosis was the leading cause of ARF and was associated with the highest mortality. Factors associated with increased mortality included: (1) peak serum creatinine greater than 3 mg/dl, (2) multiple liver transplants and (3) the need for dialysis. Pretransplant renal failure did not increase mortality. Chronic renal failure developed in 83% of patients at latest follow-up (mean: 30.5 +/- 7.9 months).
Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution (2021)

The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA, leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisulfite-treated DNA, we applied a new enzymatic deamination approach, termed enzymatic methyl-seq (EM-seq), to long-range sequencing technologies. Our methodology, named long-read enzymatic modification sequencing (LR-EM-seq), preserves the integrity of DNA, allowing long-range methylation profiling of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) over multikilobase length of genomic DNA. When applied to known differentially methylated regions (DMRs), LR-EM-seq achieves phasing of >5 kb, resulting in broader and better defined DMRs compared with that previously reported. This result showed the importance of phasing methylation for biologically relevant questions and the applicability of LR-EM-seq for long-range epigenetic analysis at single-molecule and single-nucleotide resolution.
GRIN2B encephalopathy: novel findings on phenotype, variant clustering, functional consequences and treatment aspects (2017)

In addition to previously known features of intellectual disability, epilepsy and autism, we found evidence that <i>GRIN2B</i> encephalopathy is also frequently associated with movement disorder, cortical visual impairment and MCD revealing novel phenotypic consequences of channelopathies.
Totally gasless transoral video-assisted thyroidectomy: initial report of 24 cases (2020)

Objective
To evaluate the feasibility of the gasless transoral endoscopic thyroidectomy using an innovative space maintaining method.


Methods
From Dec. 2018 to Apr. 2019, patients from Anhui Tumor Hospital treated with gasless transoral endoscopic thyroidectomy were retrospectively analyzed. Index such as intraoperative blood loss, operative time, postoperative hospital stay, and complications were recorded.


Results
A total of 24 patients were included into this analysis. All operations were successfully completed. The mean blood loss was (41.3±26.4) ml, operation time was (191.8±40.8) min, postoperative hospital stay was (6.3±1.0) d. Nobody had drinking cough, recurrent laryngeal nerve palsy, massive bleeding, hypoparathyroidism or infection with use of preventive antibacteria. Transient lower jaw numbness was found in 8 patients and almost recovered within one month.


Conclusions
Gasless transoral endoscopic thyroidectomy with the suspension device seems to be feasible and safe. Further study is needed to verify its validity.


Key words: 
Thyroidectomy; Gasless; Endoscopic; Transoral
Deuteriodifluoromethylation and gem‐Difluoroalkenylation of Aldehydes Using ClCF2H in Continuous Flow (2020)

Abstract The deuteriodifluoromethyl group (CF 2 D) represents a challenging functional group due to difficult deuterium incorporation and unavailability of precursor reagents. Herein, we report the use of chlorodifluoromethane (ClCF 2 H) gas in the continuous flow deuteriodifluoromethylation and gem ‐difluoroalkenylation of aldehydes. Mechanistic studies revealed that the difluorinated oxaphosphetane (OPA) intermediate can proceed via alkaline hydrolysis in the presence of D 2 O to provide α‐deuteriodifluoromethylated benzyl alcohols or undergo a retro [2+2] cycloaddition under thermal conditions to provide the gem ‐difluoroalkenylated product.
Self‐Assembly of Giant Unilamellar Vesicles by Film Hydration Methodologies (2019)

Self-assembly of lipids or polymeric amphiphiles into vesicular structures has been achieved by various methods since the first generation of liposomes in the 1960s. Vesicles can be obtained with diameters from the nanometer to the micrometer regime. From the perspective of cell mimicking, vesicles with diameters of several micrometers are most relevant. These vesicles are called giant unilamellar vesicles (GUVs). Commonly used methods to form GUVs are solvent-displacement techniques, especially since the development of microfluidics. These methodologies however, trap undesirable organic solvents in their membrane as well as other potentially undesired additives (surfactants, polyelectrolytes, polymers, etc.). In contrast to those strategies, summarized herein are solvent-free approaches as suitable clean alternatives. The vesicles are formed from a dry thin layer of the lipid or amphiphilic polymers and are hydrated in aqueous media using the entropically favored self-assembly of amphiphiles into GUVs. The rearrangement of the amphiphilic films into vesicular structures is usually aided by shear forces such as an alternative current (electroformation) or the swelling of water-soluble polymeric supports (gel-assisted hydration).
Data from Targeting of Hematologic Malignancies with PTC299, A Novel Potent Inhibitor of Dihydroorotate Dehydrogenase with Favorable Pharmaceutical Properties (2023)

&lt;div&gt;Abstract&lt;p&gt;PTC299 was identified as an inhibitor of VEGFA mRNA translation in a phenotypic screen and evaluated in the clinic for treatment of solid tumors. To guide precision cancer treatment, we performed extensive biological characterization of the activity of PTC299 and demonstrated that inhibition of VEGF production and cell proliferation by PTC299 is linked to a decrease in uridine nucleotides by targeting dihydroorotate dehydrogenase (DHODH), a rate-limiting enzyme for &lt;i&gt;de novo&lt;/i&gt; pyrimidine nucleotide synthesis. Unlike previously reported DHODH inhibitors that were identified using &lt;i&gt;in vitro&lt;/i&gt; enzyme assays, PTC299 is a more potent inhibitor of DHODH in isolated mitochondria suggesting that mitochondrial membrane lipid engagement in the DHODH conformation &lt;i&gt;in situ&lt;/i&gt; is required for its optimal activity. PTC299 has broad and potent activity against hematologic cancer cells in preclinical models, reflecting a reduced pyrimidine nucleotide salvage pathway in leukemia cells. Archived serum samples from patients treated with PTC299 demonstrated increased levels of dihydroorotate, the substrate of DHODH, indicating target engagement in patients. PTC299 has advantages over previously reported DHODH inhibitors, including greater potency, good oral bioavailability, and lack of off-target kinase inhibition and myelosuppression, and thus may be useful for the targeted treatment of hematologic malignancies.&lt;/p&gt;&lt;/div&gt;
Phase‐preserved macroscopic visible‐light carpet cloaking beyond two dimensions (2015)

Abstract Transformation optics, a recent geometrical design strategy of light manipulation with both ray trajectories and optical phase controlled simultaneously, promises an invisibility cloaking device that can render a macroscopic object invisible even to a scientific instrument measuring optical phase. Recent “carpet” cloaks have extended their cloaking capability to broadband frequency ranges and macroscopic scales, but they only demonstrated the recovery of ray trajectories after passing through the cloaks, while whether the optical phase would reveal their existence still remains unverified. In this paper, a phase‐preserved macroscopic visible‐light carpet cloak is demonstrated in a geometrical construction beyond two dimensions. As an extension of previous two‐dimensional (2D) macroscopic carpet cloaks, this almost‐three‐dimensional carpet cloak exhibits three‐dimensional (3D) invisibility for illumination near its center (i.e. with a limited field of view), and its ideal wide‐angle invisibility performance is preserved in multiple 2D planes intersecting in the 3D space. Optical path length is measured with a broadband pulsed‐laser interferometer, which provides unique experimental evidence on the geometrical nature of transformation optics. image
Selection of Noble Gas Binary Mixtures for Brayton Space Nuclear Power Systems (2006)

Binary noble gas mixtures are more suitable working fluids than pure gases for use in nuclear reactor space power systems, with Closed Brayton Cycle (CBC) engines. Helium has the best thermal properties but the smallest molecular weight, which increases the aerodynamic loading and hence, the size and mass of the turbomachinery. Mixing He with heavier gases of Krypton (Kr) and Xenon (Xe) to molecular weights of
Pyocyanin Production by Pseudomonas aeruginosa Induces Neutrophil Apoptosis and Impairs Neutrophil-Mediated Host Defenses In Vivo (2005)

Clearance of neutrophils from inflamed sites is critical for resolution of inflammation, but pathogen-driven neutrophil apoptosis can impair host defenses. We previously showed that pyocyanin, a phenazine toxic metabolite produced by Pseudomonas aeruginosa, accelerates neutrophil apoptosis in vitro. We compared wild-type and pyocyanin-deficient strains of P. aeruginosa in a murine model of acute pneumonia. Intratracheal instillation of either strain of P. aeruginosa caused a rapid increase in bronchoalveolar lavage neutrophil counts up to 18 h after infection. In wild-type infection, neutrophil numbers then declined steadily, whereas neutrophil numbers increased up to 48 h in mice infected with pyocyanin-deficient P. aeruginosa. In keeping with these differences, pyocyanin production was associated with reduced bacterial clearance from the lungs. Neutrophil apoptosis was increased in mice infected with wild-type compared with the phenazine-deficient strain or two further strains that lack pyocyanin production, but produce other phenazines. Concentrations of potent neutrophil chemokines (MIP-2, KC) and cytokines (IL-6, IL-1beta) were significantly lower in wild-type compared with phenazine-deficient strain-infected mice at 18 h. We conclude that pyocyanin production by P. aeruginosa suppresses the acute inflammatory response by pathogen-driven acceleration of neutrophil apoptosis and by reducing local inflammation, and that this is advantageous for bacterial survival.
Generalized Consensus and Paxos (2005)

Consensus has been regarded as the fundamental problem that must be solved to implement a fault-tolerant distributed system. However, only a weaker problem than traditional consensus need be solved. We generalize the consensus problem to include both traditional consensus and this weaker version. A straightforward generalization of the Paxos consensus algorithm implements general consensus. The generalizations of consensus and of the Paxos algorithm require a mathematical detour de force into a type of object called a command-structure set.
A ‘two-point’ bound zinc porphyrin–zinc phthalocyanine–fullerene supramolecular triad for sequential energy and electron transfer (2013)

A novel supramolecular triad composed of a zinc porphyrin-zinc phthalocyanine dyad and fullerenes has been assembled using a 'two-point' axial binding approach, and occurrence of efficient photoinduced energy transfer followed by electron transfer is demonstrated.
Nonlinear distortion of short pulses radiated by plane and focused circular pistons (1997)

Detailed measurements of finite-amplitude pulses radiated by plane and focused circular pistons in water are presented. Comparisons of time waveforms and frequency spectra, both on and off axis, are made with numerical calculations based on the nonlinear parabolic wave equation. Emphasis is on nonlinear distortion of amplitude- and frequency-modulated tone bursts. Use of short pulses enabled resolution of the direct and diffracted waves prior to their coalescence and subsequent shock formation along the axis of the source. Because of its relevance to investigations of cavitation inception, attention is devoted to variation of the peak positive (p+) and negative (p-) pressures along the axis of a focused source. It is shown that with increasing source amplitude, the maximum of each shifts away from the focal plane, toward the source. This effect is more pronounced for p- than for p+.
Bariatric surgery for diabetes: The International Diabetes Federation takes a position (2011)

Type 2 diabetes (T2D) and obesity are both complex and chronic medical disorders, each with an escalating worldwide prevalence. When obesity is severe, and/or available medical therapies fail to control the diabetes, bariatric surgery becomes a cost-effective therapy for T2D. When there are other major comorbidities and cardiovascular risk, the option of bariatric surgery becomes even more worthy of consideration. National guidelines for bariatric surgery need to be developed and implemented for people with T2D. With this in mind, the International Diabetes Federation convened a multidisciplinary working group to develop a position statement. The key recommendations cover describing those eligible for surgery and who should be prioritized, incorporating bariatric surgery into T2D treatment algorithms, performing surgery in centers with multidisciplinary teams that are experienced in the management of both obesity and diabetes, and developing bariatric surgery registries and reporting standards.
J/ψ production as a function of charged-particle pseudorapidity density in p–Pb collisions at sNN=5.02TeV (2017)

We report measurements of the inclusive J/ yield and average transverse momentum as a function of charged-particle pseudorapidity density dN ch /d in p-Pb collisions at s NN = 5.02 TeV with ALICE at the LHC. The observables are normalised to their corresponding averages in non-single diffractive events.
Damage-free metrology of porous low-k dielectrics using CD-SEM (2004)

Copper damascene process and interlayer dielectrics with ultra-low permittivity have been introduced for manufacturing future devices with higher function speed. As materials with permittivity values lower than 2.2 are required, several kinds of porous materials have been proposed as candidates. However, these porous materials have been observed to shrink easily during CD (critical dimension) measurements with a CD-SEM. To solve this problem, the mechanism of shrinkage and the solution for damage-free SEM observation condition was studied. The shrinkage caused by different electron beam irradiation conditions in a CD-SEM (S-9260, Hitachi High-Technologies Corporation) was investigated with an atomic force microscope (AFM). The result shows that the shrinkage depends on the energy and the dose of electron irradiation. In addition, the change of chemical states and composition caused by electron beam irradiation was analyzed and the shrinkage mechanism was studied. The optimum electron beam irradiation conditions for damage-free measurement are proposed based on experimental results.
Fatigue Testing of Copper Nanoparticle-Based Joints and Bonds (2021)

Abstract Fused or sintered Cu nanoparticle structures are potential alternatives to solder for ultrafine pitch flip chip assembly and to sintered Ag for heat sink attach in high-temperature micro-electronics. Meaningful testing and interpretation of test results in terms of what to expect under realistic use conditions do, however, require a mechanistic picture of degradation and damage mechanisms. As far as fatigue goes, such a picture is starting to emerge. The porosity of sintered nanoparticle structures significantly affects their behavior in cycling. The very different sensitivities to parameters, compared to solder, mean new protocols will be required for the assessment of reliability. This study focused on fatigue in both isothermal and thermal cycling. During the latter, all damage occurs at the low-temperature extreme, so life is particularly sensitive to the minimum temperature and any dwell there. Variations in the maximum temperature up to 125 °C did not affect, but a maximum temperature of 200 °C led to much faster damage. Depending on particle size and sintering conditions, deformation and damage properties may also degrade rapidly over time. Our picture allows for recommendations as to more relevant test protocols for vibration, thermal cycling, and combinations of these, including effects of aging, as well as for generalization of test results and comparisons in terms of anticipated behavior under realistic long-term use conditions. Also, the fatigue life seems to vary with the ultimate strength, meaning that simple strength testing becomes a convenient reference in materials and process optimization.
112&#x00D7;112 Gb/s transmission over 9,360 km with channel spacing set to the baud rate (360% spectral efficiency) (2010)

We transmit 112×112 Gb/s pre-filtered PDM RZ-QPSK channels with 360% spectral efficiency over 9,360km with the channel spacing set to the baud rate. This results in a record spectral efficiency for transpacific distance.
Dual Regulation Of Somatostatin Receptor Subtype 1 Gene Expression By Pit-1 In Anterior Pituitary GH3 Cells (2000)

Somatostatin represents a major release inhibiting factor for hypophyseal hormones and mediates its action via five receptor subtypes, sst1-sst5, that are all present in the anterior pituitary. The pituitary specific transcription factor Pit-1 is essential for the pituitary development and pituitary-specific gene expression. Here the transcriptional regulation of the sst1 gene, which contains putative Pit-1-binding sites, was studied in anterior pituitary GH3 cells. We found that a fragment of 2 kb suffices to drive the expression of a reporter gene specifically in this cell line. Positive and negative cis-regulatory elements contributed to the promoter activity. Among these elements two functional binding sites for Pit-1 were identified. While the proximal site mediated transcriptional activation, the distal site attenuated transcription of reporter gene constructs. Mutations of the proximal Pit-1 site prevented expression of the reporter gene. Targeting Pit-1 mRNA by antisense oligonucleotides caused inhibition of transcription of reporter gene constructs containing the proximal Pit-1-binding site. Moreover, the expression of the endogenous sst1 gene in GH3 anterior pituitary cells was blocked. This resulted in reduced sst1 levels at the plasma membrane. Reduced sst1 levels were associated with a diminished antisecretory response to the sst1-specific agonist CH-275 and somatostatin. These results demonstrate the importance of Pit-1 for the expression of the sst1 gene, which hence is placed under common genetic control with the genes for hypophysiotropic hormones and the gene for the receptor of GH-releasing hormone.
The Quantitative Anatomy of the Atlas (1994)

These measurements indicated remarkably constant dimensions for the ring itself, suggesting there may be significant functional restraints on the canal size of this unique vertebra. In contrast, a significant variability was noted in objective measurements of lateral mass height and sagittal plane widths of the entire bone.
Broadband circularly polarized corner-truncated square patch array antenna (2003)

A circularly polarized antenna with low cost foam substrate and film is proposed to obtain wide bandwidth and high performance. The proposed antenna is composed of stacked corner-truncated patches with sequential rotation feed. Having above 20% return loss and axial ratio bandwidths, the designed antenna can be used for application of a broadband system using circular polarization. And, as low cost foam and film is used for the substrate, a low cost antenna can be designed.