gebhart/patrepeval huggingface dataset:
Mega-scale experimental analysis of protein folding stability in biology and protein design (2022)

Abstract Advances in DNA sequencing and machine learning are illuminating protein sequences and structures on an enormous scale. However, the energetics driving folding are invisible in these structures and remain largely unknown. The hidden thermodynamics of folding can drive disease, shape protein evolution, and guide protein engineering, and new approaches are needed to reveal these thermodynamics for every sequence and structure. We present cDNA display proteolysis, a new method for measuring thermodynamic folding stability for up to 900,000 protein domains in a one-week experiment. From 1.8 million measurements in total, we curated a set of ~850,000 high-quality folding stabilities covering all single amino acid variants and selected double mutants of 354 natural and 188 de novo designed protein domains 40-72 amino acids in length. Using this immense dataset, we quantified (1) environmental factors influencing amino acid fitness, (2) thermodynamic couplings (including unexpected interactions) between protein sites, and (3) the global divergence between evolutionary amino acid usage and protein folding stability. We also examined how our approach could identify stability determinants in designed proteins and evaluate design methods. The cDNA display proteolysis method is fast, accurate, and uniquely scalable, and promises to reveal the quantitative rules for how amino acid sequences encode folding stability. One-Sentence Summary Massively parallel measurement of protein folding stability by cDNA display proteolysis
Isıl İşlemin Odun Özellikleri Üzerine Etkisi (2009)

Tarihe baktığımızda ahşap iğneden kilise inşaatına kadar geniş bir kullanım alanı bulmuştur. Ancakahşap ile çalışırken nem içeriğindeki değişme sebebiyle anizotropik daralma ve genişleme kombinasyonundahigroskopik özellikler sergilemesi bazı sakıncalar ortaya çıkarır. Boyutsal stabilitedeki probleme ilavetenbiyolojik saldırılar da önem arz etmektedir. Ahşabı mantar ve böceklere karşı korumak için zehirli kimyasalmaddelerle emprenye edilmesi yaygın olarak kullanılan koruma metotlarından birisidir. Ancak bu şekildekoruma; diğer organizmalar için zehirli olması, boyutsal stabiliteyi önlememesi veya boyutsal stabilitesağlayan emprenye metotlarının pahalı olması ve bu maddelerin çevreye etkilerinin sorgulanabilir olmasınedeniyle dezavantajlara sahiptir. Son 20 yılda çevresel farkındalıktaki artma nedeniyle çevreye zararlıemprenye maddelerinin kullanımında gittikçe artan şekilde kısıtlamalar ortaya çıkmaktadır. Bu durumkeresteyi biyolojik bozunmaya karşı koruyan ve boyutsal stabilitesini arttıran çevreye dost yeni metotlarıngelişmesine yol açmıştır.Bu çalışmada; ısıl işlem uygulaması süresince odunda neler oluyor? ve ısıl işlem uygulaması odunözelliklerini nasıl etkiliyor? sorularına faydalı cevaplar aranarak ısıl işlem hakkında temel bir bilgi aktarımısunulmuştur.
The Nature of Numbers: Real Computing (2022)

While studying the computable real numbers as a professional mathematician, I came to see the computable reals, and not the real numbers as usually presented in undergraduate real analysis classes, as the natural culmination of my evolving understanding of numbers as a schoolchild. This paper attempts to trace and explain that evolution. The first part recounts the nature of numbers as they were presented to us grade-school children. In particular, the introduction of square roots induced a step change in my understanding of numbers. Another incident gave me insight into the brilliance of Alan Turing in his paper introducing both the computable real numbers and his famous ``Turing machine''. The final part of this paper describes the computable real numbers in enough detail to supplement the usual undergraduate real analysis class. An appendix presents programs that implement the examples in the text.
Convolution fitting and deconvolution methods for fluorine depth profiling by resonant NRA (1997)

The 19F(p,αγ)16O resonant nuclear reaction at a proton energy of 872 keV is used to study the fluorine penetration in archaeological flints and other materials. The experimentally acquired data presented as the γ-ray yield curve Y(E) is the convolution of the fluorine depth profile, C(x), with the excitation peak G(E,x). G(E,x) changes its centroid and width with depth x due to energy loss and energy straggling. G(E,x) is obtained by measuring the γ-ray yield curves of a thin layer of calcium fluoride covered by varying thicknesses of SiO2, and fitted to a Pearson function. Two numerical techniques, namely, the convolution fitting and deconvolution method, have been developed to extract the depth profile C(x) from the experimental data. The performance and application of each method are discussed.
Mechanisms of weight maintenance under high‐ and low‐protein, low‐glycaemic index diets (2011)

Semantic network analysis of the 12 regulated proteins revealed that under an HP/LGI an anti-atherogenic effect and alterations of fat metabolism were associated with the success of maintaining the initial weight loss.
Cells, drugs and NMR (2019)

Nuclear magnetic resonance (NMR) spectroscopy is a versatile tool for investigating cellular structures and their compositions. While in vivo and whole-cell NMR have a long tradition in cell-based approaches, high-resolution in-cell NMR spectroscopy is a new addition to these methods. In recent years, technological advancements in multiple areas provided converging benefits for cellular MR applications, especially in terms of robustness, reproducibility and physiological relevance. Here, we review the use of cellular NMR methods for drug discovery purposes in academia and industry. Specifically, we discuss how developments in NMR technologies such as miniaturized bioreactors and flow-probe perfusion systems have helped to consolidate NMR's role in cell-based drug discovery efforts.
Susceptibility of a Polycaprolactone-Based Root Canal Filling Material to Degradation. I. Alkaline Hydrolysis (2005)

Polycaprolactone, a thermoplastic aliphatic polyester, is reportedly susceptible to both alkaline and enzymatic hydrolyzes. This screening study examined the susceptibility of Resilon, a polycaprolactone-based root filling composite, to alkaline hydrolysis. There were 15-mm diameter disks of Resilon and Obtura gutta-percha prepared by compressive molding and immersed in 20% sodium ethoxide for 20 or 60 min. Control disks were immersed in ethanol for 60 min. These disks were examined using field-emission scanning electron microscopy and energy dispersive X-ray analysis. For Resilon, the surface resinous component was hydrolyzed after 20 min of sodium ethoxide immersion, exposing the spherulitic polymer structure and subsurface glass and bismuth oxychloride fillers. More severe erosion occurred after 60 min of sodium ethoxide treatment. Gutta-percha was unaffected after immersion in sodium ethoxide. As Resilon is susceptible to alkaline hydrolysis, it is possible that enzymatic hydrolysis may occur. Biodegradation of Resilon by bacterial/salivary enzymes and endodontically relevant bacteria warrants further investigation.
Membrane-Suspended Nanocompartments Based on Ordered Pores in Alumina (2002)

Mind the gap! Freestanding membranes spanning highly ordered nanocompartments can act as mechanically stable systems for modelling cellular membranes or utilised for biosensor devices. This study used DODAB lipid membrane over an etched aluminum substrate (see the graphic). STM/SFM revealed high surface coverage and probed the mechanical stability of the suspending membranes.
On-chip hermetic packaging enabled by post-deposition electrochemical etching of polysilicon (2005)

The authors present a novel monolithic on-wafer packaging, which solves the main problems of existing monolithic encapsulation techniques for MEMS polysilicon surface micromachining. It involves the formation of a nanoporous polysilicon encapsulation layer by post-deposition electrochemical etching on top of PSG sacrificial layer, followed by removal of the sacrificial layer through the nanopores and a final vacuum sealing by depositing a polysilicon layer. Thanks to the nanopores through the thick porous polysilicon layer, the vacuum sealing is achieved by depositing a polysilicon layer as thin as 1000 /spl Aring/, and no sealing material is deposited inside the cavity. The pressure inside the sealed cavity, measured by an encapsulated polysilicon pirani gauge, was around 200 mTorr and showed no detectable leaks over 3 months.
Interaction of an alpha-melanocyte-stimulating hormone-diphtheria toxin fusion protein with melanotropin receptors in human melanoma metastases. (1992)

A hybrid toxin targeted to melanotropin receptors and selectively cytotoxic to melanoma cell lines in vitro has recently been developed. The toxin, a recombinant fusion protein (designated DAB389-MSH), contains the peptide sequences of alpha-melanocyte-stimulating hormone (alpha-MSH) and the catalytic (cytotoxic; Fragment A) and lipophilic (part of Fragment B) domains of diphtheria toxin. In the present study, binding of DAB389-MSH to melanotropin receptors in biopsy specimens of human and mouse melanoma metastases was assessed by measuring its ability to inhibit binding of a radiolabeled, superpotent analogue of alpha-MSH (125I-[Nle4,D-Phe7]-alpha-MSH; 125I-NDP-MSH) and comparing its potency in this system with those of the established ligands NDP-MSH and alpha-MSH. Radioligand binding to tissue sections in vitro was localized and quantified by autoradiography and image analysis. DAB389-MSH inhibited binding of 125I-NDP-MSH to experimental murine B16-F1C23 melanoma metastasis tissue and to melanoma metastases of three patients. In both mouse and human melanoma tissues, concentration-response relationships for DAB389-MSH-mediated inhibition of 125I-NDP-MSH binding were parallel, and its maximal effects were comparable in magnitude, to those of NDP-MSH and alpha-MSH. Half-maximal peptide concentrations for inhibition of 125I-NDP-MSH binding to mouse melanoma tissue sections were: NDP-MSH, 0.63 nM; alpha-MSH, 3.14 nM; and DAB389-MSH, 10.1 nM. In human melanoma tissues, the respective half-maximal peptide concentrations for inhibition of 125I-NDP-MSH binding to mouse melanoma tissue sections were: NDP-MSH, 1.80 nM; alpha-MSH, 2.43 nM; and DAB389-MSH, 11.9 nM. Taken together, these results suggest that NDP-MSH, alpha-MSH, and DAB389-MSH bind to a common melanotropin receptor in human metastatic melanoma cells. Since previous work has shown that melanotropin receptors are detectable in melanoma metastases of about 80% of human patients, malignant melanoma cells of many patients may be susceptible to killing by the melanotropin receptor-targeted cytotoxin DAB389-MSH.
3,5-bis(styryl)pyrazole inhibits mitosis and induces cell death independent of BubR1 and p53 levels by depolymerizing microtubules (2023)

Here, we show that 3,5-bis[(1E)-2-(2,6-dichlorophenyl)ethenyl]-1H-pyrazole 2l depolymerizes microtubules and reduces the number of growing tips of microtubules. The fluorescence recovery after photobleaching experiment in live MCF-7 cells showed that pyrazole 2l suppresses spindle microtubule dynamics. Further, the compound inhibits chromosome movements, activates the spindle assembly checkpoint and blocks mitosis in MCF-7 cells. Pyrazole 2l treatment induced cell death in a variety of pathways. Pyrazole 2l induces cell death independent of BubR1 and p53 levels of MCF-7 cells upon microtubule depolymerization. Further, pyrazole 2l increases the interaction between NF-κB and microtubules and enhances the nuclear localization of NF-κB at its half-maximal proliferation inhibitory concentration while a high concentration of the compound reduced the nuclear localization of NF-κB. Interestingly, the compound exerted significantly stronger antiproliferative effects in cancerous cells than in non-cancerous cells. The results indicated that pyrazole 2l inhibits mitosis by targeting microtubules, induces several types of cell death stimuli and suggests its potential as a lead in developing anticancer agent.
Cardiac steatosis potentiates angiotensin II effects in the heart (2014)

Lipid accumulation in the heart is associated with obesity and diabetes and may play an important role in the pathogenesis of heart failure. The renin-angiotensin system is also thought to contribute to cardiovascular morbidity in obese and diabetic patients. We hypothesized that the presence of lipid within the myocyte might potentiate the cardiomyopathic effects of ANG II in the cardiac diacylglycerol acyl transferase 1 (DGAT1) transgenic mouse model of myocyte steatosis. Treatment with ANG II resulted in a similar increase in blood pressure in both nontransgenic and DGAT1 transgenic mice. However, ANG II in DGAT1 transgenic mice resulted in a marked increase in interstitial fibrosis and a reduction in systolic function compared with nontransgenic littermates. Lipidomic analysis revealed that >20% of lipid species were significantly altered between nontransgenic and DGAT1 transgenic animals, whereas 3% were responsive to ANG II administration. ROS were also increased by ANG II in DGAT1 transgenic hearts. ANG II treatment resulted in increased expression of transforming growth factor (TGF)-β2 and the type I TGF-β receptor as well as increased phosphorylation of Smad2 in DGAT1 transgenic hearts. Injection of neutralizing antibodies to TGF-β resulted in a reduction in fibrosis in DGAT1 transgenic hearts treated with ANG II. These results suggest that myocyte steatosis amplifies the fibrotic effects of ANG II through mechanisms that involve activation of TGF-β signaling and increased production of ROS.
Preparation and characterization of a temperature‐sensitive nonwoven poly(propylene) with increased affinity for guest molecules (2014)

ABSTRACT A temperature‐sensitive hydrogel with the capability of inclusion complex formation with guest molecules was successfully grafted onto the surface of nonwoven polypropylene (nonwoven PP). This was carried out by the use of N ‐isopropylacrylamide monomer and a modified cyclodextrin (acrylamidomethyl‐β‐cyclodextrin (β‐CD‐NMA)). Fourier‐transform infra red (FT‐IR) and elemental analyses confirmed the presence of poly( N ‐isopropylacrylamide) (PNIPAAm) and β‐CD‐NMA components on the surface of the textile. Equilibrium swelling ratio measurements showed that the grafted hydrogel maintained its temperature‐sensitive property compared to a nongrafted hydrogel. The effect of β‐CD‐NMA and crosslink agent concentrations on the grafting yield was studied. The β‐CD‐NMA content into the PNIPPAM‐ β‐CD‐NMA grafted nonwoven PP (PNIPAAm‐β‐CD‐NMA‐PP) was estimated by FT‐IR through a new procedure. The estimated amounts of β‐CD‐NMA in PNIPAAm‐β‐CD‐NMA‐PP were determined to be 0.9, 1.9 mg g −1 for 0.019 M and 0.049 M concentrations of β‐CD‐NMA in monomer solution, respectively. The PNIPAAm‐β‐CD‐NMA‐PP showed a remarkable increase in absorbance affinity of 8‐anilino‐1‐naphthalenesulfonic acid ammonium salt at 20°C from 0.93 to 3.33 µmol g −1 compared to PNIPAAm‐PP. Furthermore, the results showed a temperature‐sensitive loading affinity for PNIPAAm‐β‐CD‐NMA‐PP in absorbance of guest molecules due to the presence of β‐CD‐NMA. The use of hydrophobic guest molecules such as fragrance oils and antibiotics in modified fabrics can provide new applications in textile and pharmaceutical industry. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 40497.
Site-specific 68Ga-labeled nanobody for PET imaging of CD70 expression in preclinical tumor models (2023)

[<sup>68</sup>Ga]Ga-NOTA-anti-CD70 VHH showed excellent in vivo targeting of CD70 in human cancer xenografts. PET imaging using this radioimmunoconjugate holds promise as a non-invasive method to identify and longitudinally follow-up patients who will benefit most from anti-CD70 therapies.
An active microelectronic transducer for enabling label-free miniaturized chemical sensors (2002)

A device is described that enables the rapid sensing of molecules with a high degree of sensitivity and selectivity. This device is based on a depletion mode FET in which the gate electrode has been removed, certain molecular receptor species (e.g. proteins, oligonucleotides, antibodies, etc.) have been affixed, and a test solution is exposed to the gate. A counter electrode is immersed in the solution in order to establish a reference potential. Changes in the source-drain current indicate an attachment response of the system. Preliminary results are presented.
Hearing, vocalization and the external ear of a marsupial, the Northern Quoll, Dasyurus hallucatus (1994)

As part of a continuing study of the development of the marsupial auditory system, auditory brainstem responses (ABR) were recorded and an ABR audiogram was constructed for five female Northern Quolls (Dasyurus hallucatus), which are nocturnal carnivores. The best frequency for hearing lies between 8 and 10 kHz, and at 50 dB SPL there is a range from about 0.5 to 40 kHz. Vocalizations of adult quolls and pouch-young were recorded with a digital audio tape recorder, and the power spectra of representative calls were compared with the ABR audiogram. The common adult vocalizations have most energy at the lower end of the hearing range, whereas frequencies that are dominant in the isolation calls of the pouch-young lie close to the best frequency of hearing. Samples of nocturnal sounds of the habitat of the quoll were also recorded and analyzed. Power spectra have peak energy at frequencies between 2 and 5 kHz, with a smaller contribution above 10 kHz. The spectrum contains relatively little power at the best frequency of hearing. Measurements of the sound pressure level at the external ear canal as a function of stimulus frequency and location in space suggest that the directional amplifying properties of the pinna will operate most effectively on sound frequencies at the upper end of the quoll's hearing range, a region that may be important in prey detection. Comparisons are made with other mammalian nocturnal carnivores and with other marsupials. We speculate that, for nocturnal carnivores, one role of the low-frequency part of the hearing range concerns the recognition of adult conspecifics, the mid-frequency range is important for the detection of pouch-young, and the upper range may be particularly concerned with prey/predator detection.
Cathodoluminescence of Strontium Oxide, Barium-Strontium Oxide, and Magnesium Oxide (1958)

A survey of some spectral and time decay properties of the cathodoluminescence of SrO, (BaSr)O, and MgO samples has been made in sealed-off high-vacuum tubes in the spectral range from 220 m\ensuremath{\mu} to 600 m\ensuremath{\mu}. Observations were made for sample temperatures varying from 90\ifmmode^\circ\else\textdegree\fi{}K to room temperature and above with the samples in different states of thermionic activity.In SrO samples, luminescence maxima were observed at photon energies of 4.9 ev, 3.7 ev, 3.2 ev, and 2.4 ev. The 4.9-ev band intensity increases with the thermionic activity of the sample whereas that of the 3.2-ev band decreases.Emission band maxima were found in (BaSr)O at energies of 4.0 ev, 3.1 ev, 2.6 ev, and 2.1 ev. A comparison of the (BaSr)O luminescence is made with that from SrO and BaO.MgO samples were studied in both polycrystalline and single crystal forms. Luminescence band maxima were observed at energies of 5.2 ev, 3.6 ev, 2.7 ev, 2.3 ev, and 2.1 ev. The 2.3-ev band may be enhanced by heating the sample in magnesium vapor or diminished by heating it in oxygen.Suggestions are made concerning possible electronic mechanisms giving rise to some of the above bands on the basis of the temperature dependence of their intensities and their types of afterglow.
The impact of cancer therapy on cognition in the elderly (2013)

Cancer and cancer therapy-related cognitive impairment (formerly known as chemobrain or chemo-fog) are often described in the literature. In the past, studies have failed to prove the existence of cancer therapy-related cognitive dysfunction. However, more recently, prospective trials have shown that patients undergoing chemotherapy do display impairment in specific cognitive domains. Aging confers an increased risk of developing cancer, as well as cognitive impairment. The Geriatric Oncology clinic of the Segal Cancer Centre, Jewish General Hospital in Montreal was founded in 2006 to address the unique needs of older cancer patients. We will describe two cases of cancer therapy-related cognitive impairment from our Geriatric Oncology clinic. The first case is that of a 75 year old male diagnosed with stage III non-small cell lung carcinoma who complained of forgetfulness since starting carboplatin-paclitaxel. The second case is that of a 65 year old female diagnosed with stage I, estrogen-receptor-positive breast cancer who had undergone lumpectomy followed by adjuvant cyclophosphamide, methotrexate and fluorouracil chemotherapy, radiation therapy and was on exemestane when she was evaluated. We will also briefly review the literature of cancer therapy-related cognitive impairment.
A Straightforward and Versatile Synthetic Approach to 1‐Azabicyclic Alkaloids. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Recovering ferromagnetic metal surfaces to fully exploit chemistry in molecular spintronics (2015)

Organic spintronics is a new emerging field that promises to offer the full potential of chemistry to spintronics, as for example high versatility through chemical engineering and simple low cost processing. However, one key challenge that remains to be unlocked for further applications is the high incompatibility between spintronics key materials such as high Curie temperature Co, Ni, Fe (and their alloys) and wet chemistry. Indeed, the transition metal proneness to oxidation has so far hampered the integration of wet chemistry processes into the development of room temperature organic spintronics devices. As a result, they had mainly to rely on high vacuum physical processes, restraining the choice of available organic materials to a small set of sublimable molecules. In this letter, focusing on cobalt as an example, we show a wet chemistry method to easily and selectively recover a metallic surface from an air exposed oxidized surface for further integration into spintronics devices. The oxide etching process, using a glycolic acid based solution, proceeds without increasing the surface roughness and allows the retrieval of an oxygen-free chemically active cobalt layer. This unlocks the full potential of wet chemistry processes towards room temperature molecular spintronics with transition metals electrodes. We demonstrate this by the grafting of alkylthiols self-assembled monolayers on recovered oxidized cobalt surfaces.
The Synthesis of a Novel Phosphorus Containing Antigen (2001)

Antigen 12, containing a phosphonyl peptide hapten with free C-terminal carboxylic group, was synthesized by 11 reaction steps. The design of the hapten was based on the transition state of peptide hydrolysis catalyzed by carboxypeptidase A.
Narrow-linewidth, Yb 3+ -doped, hybrid microstructured fibre laser operating at 1178 nm (2009)

A narrow-linewidth fibre laser operating at 1178 nm that employs a double-clad Yb3+-doped hybrid microstructured fibre, is demonstrated. The fibre suppresses amplified spontaneous emission by the photonic bandgap effect, and parasitic lasing at shorter wavelength range (1030–1100 nm) was prevented. A narrow-linewidth (&lt;0.05 nm), CW output of 0.5 W at 1178 nm with a slope efficiency of 14%, was measured.