gebhart/patrepeval huggingface dataset:
Parallel analysis of mutant human glucose 6‐phosphate dehydrogenase in yeast using PCR colonies (2005)

We demonstrate a highly parallel strategy to analyze the impact of single nucleotide mutations on protein function. Using our method, it is possible to screen a population and quickly identify a subset of functionally interesting mutants. Our method utilizes a combination of yeast functional complementation, growth competition of mutant pools, and polymerase colonies. A defined mutant human glucose-6-phosphate-dehydrogenase library was constructed which contains all possible single nucleotide missense mutations in the eight-residue glucose-6-phosphate binding peptide of the enzyme. Mutant human enzymes were expressed in a zwf1 (gene encoding yeast homologue) deletion strain of Saccharomyces cerevisiae. Growth rates of the 54 mutant strains arising from this library were measured in parallel in conditions selective for active hG6PD. Several residues were identified which tolerated no mutations (Asp200, His201 and Lys205) and two (Ile199 and Leu203) tolerated several substitutions. Arg198, Tyr202, and Gly204 tolerated only 1-2 specific substitutions. Generalizing from the positions of tolerated and non-tolerated amino acid substitutions, hypotheses were generated about the functional role of specific residues, which could, potentially, be tested using higher resolution/lower throughput methods.
Different Sensitivity to Adrenocorticotropin of Dispersed Adrenocortical Cells from Patients with Cushing's Disease with Macronodular and Diffuse Adrenal Hyperplasia* (1984)

A patient with Cushing's syndrome and low plasma ACTH levels had a unilateral adrenal mass (diameter, 3 cm), which proved to consist of adenomatous hyperplasia. Dispersed adrenocortical cells prepared from this mass responded to ACTH with a maximal increment in cortisol release of more than 400%. Five months after operation Cushing's syndrome recurred. Computed tomography scanning showed an enlarged macronodular adrenal gland on the other side. The cells prepared from this adrenal gland were stimulated by ACTH by more than 600%. In adrenal glands from eight other patients with Cushing's disease cells from macroscopic nodules in hyperplastic adrenocortical tissue had increased responsiveness to ACTH in vitro, in comparison to cells from macroscopically diffuse hyperplastic adrenal tissue. The stimulability of the pituitary-adrenal axis (by metyrapone) and its suppressibility (by high dose dexamethasone) did not differ between the two groups of patients. These observations suggest that in the presence of adenomatous or macronodular adrenal hyperplasia lower circulating ACTH levels may sustain hypercortisolism than in diffuse adrenal hyperplasia. The presence of a unilateral adrenal mass and low normal plasma ACTH levels in patients with Cushing's syndrome, therefore, does not unequivocally indicate the presence of an autonomous adrenal adenoma. Tests with metyrapone and dexamethasone should still be carried out in order to make a secure differential diagnosis.
Structural Study of Hybrid Organic/Inorganic Polymer Gels Using Time-Resolved Fluorescence Probing† (2000)

Thin films made of hybrid organic/inorganic polymers, synthesized through the sol−gel method and composed of silica with grafted poly(ethylene oxide) or poly(propylene oxide) chains, are studied by time-resolved fluorescence-probing analysis. The fluorescence-probing technique is employed both to structurally characterize these nanoheterogeneous materials and to demonstrate the capacity of this technique to detect important differences in materials having approximately the same chemical structure. It is found that the films consist of interpenetrating networks of organic and inorganic domains constituting two distinguishable subphases, an organic and an inorganic one. The volume fraction of the organic phase is larger than that of the inorganic phase, and it increases with increasing poly(ethylene oxide) or poly(propylene oxide) chain length. In addition, hydrophobic interactions tend to organize the organic domain, forming organic clusters that can accommodate hydrophobic probes. This is particularly true for large polyether chains.
High-resolution analysis for urinary DNA jagged ends (2022)

Single-stranded ends of double-stranded DNA (jagged ends) are more abundant in urinary DNA than in plasma DNA. However, the lengths of jagged ends in urinary DNA remained undetermined, as a previous method used for urinary DNA jagged end sequencing analysis (Jag-seq) relied on unmethylation at CpG sites, limiting the resolution. Here, we performed high-resolution Jag-seq analysis using methylation at non-CpG cytosine sites, allowing determination of exact length of jagged ends. The urinary DNA bore longer jagged ends (~26-nt) than plasma DNA (~17-nt). The jagged end length distribution displayed 10-nt periodicities in urinary DNA, which were much less observable in plasma DNA. Amplitude of the 10-nt periodicities increased in patients with renal cell carcinoma. Heparin treatment of urine diminished the 10-nt periodicities. The urinary DNA jagged ends often extended into nucleosomal cores, suggesting potential interactions with histones. This study has thus advanced our knowledge of jagged ends in urine DNA.
Utilization of systemic therapy for treatment of advanced urothelial carcinoma: Lessons from real world experience (2021)

Metastatic bladder cancer has poor overall survival. Though systemic therapies have shown to improve overall survival, real-world studies have shown that more than half of the patients do not receive any systemic therapy, while only around 15-20% receive second-line therapy. Even in patients receiving systemic therapies a disproportionately higher use of carboplatin is observed in the first line despite proven superior effectiveness of cisplatin. Reasons for these observations include moderate effectiveness and relatively toxicity of platinum-based chemotherapy regimens, concerns with performance status and co-morbidities in this predominantly older patient population, communications barriers, lack of social support, and access to affordable healthcare. Herein we discuss potential ways to overcome these challenges which include (1) preventing/delaying metastatic disease by maximizing the receipt of neoadjuvant cisplatin-based therapy, and development of better tolerated and more effective neoadjuvant and adjuvant therapies, (2) use of avelumab maintenance therapy after 4-6 cycles of platinum-based chemotherapy to overcome attrition of patients from first to second-line therapy, (3) advancing effective and well-tolerated systemic therapies such as enfortumab vedotin, and erdafitinib to the first-line metastatic setting or even to the localized setting, (4) further development of effective and well-tolerated therapies like sacituzumab govitecan, a novel antibody-drug conjugate and (5) improving affordability and accessibility to systemic therapy agents.
A congeneric multi-sensor data fusion algorithm and its fault-tolerance (2010)

In this paper, a multi-sensor data fusion algorithm was put forward. First, based on the statistics, the standard deviation relating to the fusion value of sensors' measured data was used to estimate sensor's variance. Secondly, by using this estimate variance, a new adaptive weighted fusion algorithm for multi-sensor data fusion, as well as its iterative form, was put forward. Then, a “memory attenuation factor” was introduced to improve this algorithm to weaken the adverse effect from the old data. At last, ample simulation work was presented, in which this algorithm and the adaptive weighted estimate fusion algorithm in some references were applied with sensor no-fault and fault conditions. This result showed that this algorithm effectively captured the sensor fault character, and timely adjusted the sensor fusion weight value, so as to ensure much better fusion result. In all, this algorithm brings satisfying performance in respect of accuracy and tolerance to sensor fault for multi-sensor data fusion.
Catalytic Decomposition of Simulants for Chemical Warfare V Agents: Highly Efficient Catalysis of the Methanolysis of Phosphonothioate Esters (2006)

So gut wie das Original: Mit metallhaltigen Systemen wie 1 gelang die sehr effektive Methanolyse von Phosphonothioaten. Die katalytische Methanolyse eines SCH2CH2NEt2-Derivats, eines Analogons des Organophosphorkampfstoffs VX, wird vorhergesagt. Zudem wird gezeigt, dass bei der katalysierten Methanolyse von S-(3,5-Dichlorphenyl)-O-ethyl(methylphosphonothioat) das Arylthioat in einem konzertierten Schritt verdrängt wird (Übergangszustand 2). Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z503182_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Interspeech pathology challenge: investigations into speaker and sentence specific effects (2012)

In this paper, we report our experiments on Interspeech 2012 Speaker Trait Pathology challenge task [2]. Specifically, we investigate two factors that impact the acoustic properties of the utterances collected in this task. Although the task treats utterances as independent data points, multiple utterances are recorded from individual speakers. Furthermore, the utterances correspond to readings of 17 given written sentences. In one experiment, we attempt to reduce variation due to speaker through dimensionality reduction. While these experiments showed promising results on development set, the performance did not translate to the evaluation test. In another, we learn classifiers conditioned on the sentences to capture sentence-specific signatures. This approach showed improved performance over the baseline on development set and the improvement translated to marginal gains on evaluation set. These experiments demonstrates the need to pay attention to the independence assumptions while collecting and defining clinical tasks.
Hematologic and Blood Chemistry Data for the Chimpanzee (Pan troglodytes) (1972)

The hemogram and blood chemistry profile are reported for the chimpanzee. Data were derived from analyses of 211 blood specimens from 98 chimpanzees of both sexes and varying ages. Values recorded for the chimpanzee are, with minor variations, comparable to values reported for man.
A high performance liner for copper damascene interconnects (2001)

We describe a liner for Cu-Damascene multilevel ULSI interconnects, which satisfies all the important requirements for a high performance and reliable Cu interconnect technology. This liner is implemented in the first manufacturing process to produce and ship CMOS chips with Cu interconnects. The liner is a bilayer from a family of hcp/bcc-TaN followed by bcc-Ta (/spl alpha/-Ta), deposited sequentially in a single PVD chamber from a pure Ta target, using Ar and N/sub 2/ sputtering gases. This bilayer simultaneously maximizes adhesion to the interlevel dielectric and the Cu fill, and has very low in-plane resistivity (/spl sim/30-60 /spl mu//spl Omega/-cm, depending on TaN/Ta thicknesses). These qualities produce high-yield, highly reliable, and electromigration-redundant Cu interconnects.
Doping Mechanism and Electronic Structure of Alkali Metal Doped Tris(8-hydroxyquinoline) Aluminum (2012)

We investigated the electronic structures of alkali metal doped Alq3 molecules prepared by codeposition of Na and tris(8-hydroxyquinolinato)aluminum (Alq3) (Na:Alq3) using in situ synchrotron radiation photoelectron spectroscopy. The doping ratio of Na to Alq3 (RNa) was 0, 0.3, 0.6, 0.8, 2.7, 3.4, or 3.9. The work function, calculated from photoemission spectra, remained at 3.6 eV ± 0.03 eV for all samples, while the energy of the highest occupied molecular orbital increased from 2.2 to 2.85 eV as the doping ratio increased from RNa = 0 to RNa = 2.7. The work function and valence band spectra indicated that there is no band bending or surface work function change due to an alkali doping effect, in contrast to the findings of previous reports. The doped layer was composed of an n-type organometallic complex according to the analysis of O 1s and N 1s spectra. The N-type doping effects shown in the N 1s spectra of coevaporation samples were reflected in the schematic band diagram, so the energy difference between the Fermi level (EF) and the lowest unoccupied molecular orbital (LUMO) decreased by 0.64 eV. The schematic band diagram demonstrates that a monotonic shift of the LUMO toward EF was observed with increasing doping, which is in contrast to general n-type doping effects in inorganic semiconductors. Also, we experimentally observed increased electron transport characteristics of alkali metal doped Alq3. The operating voltage at 100 mA/cm2 decreased from 11.9 V (RNa = 0) to 9.6 V, and the luminance at 10.5 V increased from 3575 cd/m2 (RNa = 0) to 9675 cd/m2 when the Na:Alq3 film (RNa = 2.7) was inserted between Alq3 and LiF/Al.
Daylight Exposure and Circadian Efficiency in Office Rooms Equipped with Anidolic Daylighting Systems (2009)

Anidolic Daylighting Systems (ADS) typically reduce the daylight flux reaching an office roomâs window section and increase it in the rear of the room. They offer interesting possibilities for the combination of comfortable daylighting and highly energy-efficient office lighting designs. The objective of this study was to get an insight into typical ocular daylight exposures in office rooms equipped with ADS and to compare them to an artificial blue-enriched light source. Results from a recent study by Viola et al. [9] demonstrated that the use of the same light source positively influenced subjective wellbeing and sleep quality in office workers. We recorded daytime irradiance values for several weeks from April-May 2009 in an experimental office setup in our laboratory using a portable digital spectroradiometer. The artificial light sources were measured during the night. With respect to more circadian aspects of day- and artificial lighting designs we finally corrected the measured irradiances with a c(Î»)-curve. Our results showed to which extent external sky conditions influenced light exposure of office workers in an ADS-equipped office room for different sky types. The considered ADS was able to supply natural blue light irradiance levels during large parts of days with intermediate and clear skies, which were much higher than those created by our artificial lighting installation based on two blue-enriched fluorescent lamps. The same was true for weighted circadian irradiance values Eec. We conclude that for the tested ADS-equipped office room, complementary artificial lighting with blue-enriched polychromatic fluorescent tubes might be useful on days with predominantly overcast skies and before 09:00 and after 16:30 on all days.
409 Structural changes of actin cytoskeleton on micro patterned plate (2007)

chaiiges of aCtin cytoskeleton
Multiparametric magnetic resonance imaging in mucosal primary head and neck cancer: a prospective imaging biomarker study (2017)

Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12616000534482 (26 April 2016).
Abstract C94: Deubiquitylases as novel anticancer targets: Discovery and development of novel USP7 inhibitors (2009)

Abstract The ubiquitin-proteasome pathway is a complex system consisting of enzymes that conjugate or deconjugate ubiquitin to/from target proteins upstream of the 26S proteasome. In particular, ubiquitin deconjugation is performed by families of proteases known as deubiquitylating enzymes (DUBs). The therapeutic validation of the ubiquitin-proteasome system was provided by the marketing approval of bortezomib (PS-341) for the treatment of multiple myeloma (MM). In our search for alternative approaches for the treatment of MM, we investigated the therapeutic potential of inhibiting another component of the ubiquitin-proteasome pathway, the DUB USP7. Our rationale for targeting USP7 is as follows: 1) Blockade of USP7 using siRNA or homologous recombination results in elevated levels of the tumor suppressor p53 and cell cycle arrest in cancer cells. In contrast to the situation in the majority of human tumors, mutations or deletions of p53 in MM are relatively rare and thus the activation of p53 is likely to offer a therapeutic benefit in MM. 2) Knockdown of USP7 destabilizes the adaptor protein Claspin, inhibiting activation of Chk1, an effector kinase in the DNA damage response, abrogating the G2M cell cycle checkpoint and providing a mechanism for inducing tumor cell death in a p53 independent manner. Thus inhibition of USP7 would be predicted to activate pro-apoptotic and inactivate pro-survival pathways in multiple myeloma, resulting in tumor suppression. Recently, using its proprietary screening technology, Progenra discovered and characterized a small molecule inhibitor of USP7, P5091. Specifically, P5091 selectively inhibits USP7 relative to other proteases and exhibits cytotoxic activity against both p53 wild type and p53 mutant tumor cell lines. Furthermore, P5091 destabilizes the pharmacodynamic markers HDM2 and Claspin in tumor cells and induces cell death synergistically in combination with genotoxic agents. Medicinal chemistry has identified a series of potent and selective novel chemical entities. Initial preclinical studies at the Dana-Farber Cancer Institute demonstrate that P5091 induces apoptosis and is cytotoxic against human MM cells but not normal plasma cells. In conclusion, these data demonstrate that 1) USP7 is a viable target for the treatment of MM and other cancers; and 2) P5091 is an efficacious inhibitor of USP7. Preclinical development of the P5091 series continues, augmented by a comprehensive medicinal chemistry program designed to identify a clinical candidate from this series in 2010. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):C94.
2D and 3D Conceptual Magnetic Design of the MADMAX Dipole (2020)

One of the frontier of particle physics beyond the Standard Model is the research of axion-like particles, to explain the absence of CP violation in the strong interaction and to provide dark matter candidates. In the MADMAX (MAgnetized Disk and Mirror AXion) experiment, the principle of axions detection relies on the predicted emission of an electric field, picked up using dielectric disks. The electric field intensity is proportional to the square of the local magnetic field, thus the MADMAX experiment would be set up in a 9 T NbTi dipole magnet, 6.9 m in length with a bore diameter of 1.35 m. The dipole produces a Figure of Merit over the surface of the disks of 100 T <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> along 2 meters, enough to detect axions with masses in the range of 100 μeV. This paper reports the 2D and 3D conceptual magnetic design of the MADMAX dipole. Starting from the experimental principles, it introduces the design parameters, constraints, and the methodology employed, aiming at minimizing the magnet cost minimizing the cost of the conductor. Then, the 2D and 3D designs are described, focusing in particular on the cross-section resulting from the 2D optimization and the heads optimization in 3D with and without iron, made by coupling a dedicated analytical approach to genetic algorithms.
Cloud-based thermal error compensation with a federated learning approach (2022)

Thermal error compensation is one of the most research-oriented topics in manufacturing with rising importance in the industry. This paper presents an innovative Industry 4.0 application of thermal error compensation for precision engineering. A federated learning-based thermal error compensation approach running in the cloud is applied to two machine tools, one located at ETH Zürich, and another one at TU Wien. Although environmental conditions and thermal error behaviour of both machines differ, the implemented knowledge transfer across machines is a viable compensation strategy, albeit with limited precision. A detailed comparison of the two machines of the same type under the same load conditions shows foreseeable similarities in behaviour, but also clear differences due to the different configurations and lifetime status. The cloud-based compensation reduced the crucial thermal errors in the best case of both machine tools by more than 80% under critical conditions.
Uncharged Helical Modular Polypeptide Hydrogels for Cellular Scaffolds (2015)

Grafted synthetic polypeptides hold appeal for extending the range of biophysical properties achievable in synthetic extracellular matrix (ECM) hydrogels. Here, N-carboxyanhydride polypeptide, poly(γ-propargyl-l-glutamate) (PPLG) macromers were generated by fully grafting the "clickable" side chains with mixtures of short polyethylene glycol (PEG) chains terminated with inert (-OH) or reactive (maleimide and/or norbornene) groups, then reacting a fraction of these groups with an RGD cell attachment motif. A panel of synthetic hydrogels was then created by cross-linking the PPLG macromers with a 4-arm PEG star molecule. Compared to well-established PEG-only hydrogels, gels containing PPLG exhibited dramatically less dependence on swelling as a function of cross-link density. Further, PPLG-containing gels, which retain an α-helical chain conformation, were more effective than standard PEG gels in fostering attachment of a human mesenchymal stem cell (hMSC) line for a given concentration of RGD in the gel. These favorable properties of PPLG-containing PEG hydrogels suggest they may find broad use in synthetic ECM.
Selective-Area Growth of InAs Nanowires with Metal/Dielectric Composite Mask and Their Application to Vertical Surrounding-Gate Field-Effect Transistors (2013)

We attempted the selective-area metalorganic vapor-phase epitaxial (SA-MOVPE) growth of InAs nanowires (NWs) using a tungsten/dielectric composite mask and fabricated nanowire vertical surrounding-gate field-effect transistors (NW-VSG-FETs), where tungsten served as both the mask in SA-MOVPE growth and the bottom electrode of the FET. The growth of NWs with diameters as low as 100 nm was demonstrated using the composite mask. The fabricated NW-VSG-FET exhibited improved drain current density as compared with our previously reported NW-VSG-FETs, and a larger on/off ratio as compared with previously reported NW-VSG-FETs having similar electrodes at the bottoms of NWs.