gebhart/patrepeval huggingface dataset:
A camel milk whey protein rich in half‐cystine (1986)

The amino acid sequence of a recently isolated camel milk protein rich in half-cystine has been determined by peptide analyses. The 117-residue protein has 16 half-cystine residues, concluded to correspond to disulfide bridges and suggesting a tight conformation of the molecule. Comparisons of the structure with those of other proteins reveal several interesting relationships. The camel protein is clearly homologous with a previously reported rat whey phosphoprotein of possible importance for mammary gland growth regulation, and with a mouse protein of probable relationship to neurophysins. The camel, rat and mouse proteins may represent species variants from a rapidly evolving gene. Residue identities in pairwise comparisons are 40% for the camel/rat proteins and 33% for the camel/mouse proteins, with 38 positions conserved in all three forms. The camel protein also reveals an internal repeat pattern similar to that for the other two proteins. The homology between the three milk whey proteins has wide implications for further relationships. Thus, previously noticed similarities, involving either of the milk proteins, include limited similarities to casein phosphorylation sites for the camel protein, to neurophysins in repeat and half-cystine patterns for the mouse and rat proteins, and to an antiprotease for the rat protein. These similarities are reinforced by the camel protein structure and the recognition of the three whey proteins as related. Finally a few superficial similarities with the insulin family of peptides and with some other peptides of biological importance are noticed. Combined, the results relate the camel protein in a family of whey proteins, and extend suggestions of relationships with some binding proteins.
Supplementary Figure Legend from Autocrine Production of Amphiregulin Predicts Sensitivity to Both Gefitinib and Cetuximab in <i>EGFR</i> Wild-type Cancers (2023)

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Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle (2022)

The capacity of the intestinal microbiota to degrade otherwise indigestible diet components is known to greatly improve the recovery of energy from food. This has led to the hypothesis that increased digestive efficiency may underlie the contribution of the microbiota to obesity. OligoMM12-colonized gnotobiotic mice have a consistently higher fat mass than germ-free (GF) or fully colonized counterparts. We therefore investigated their food intake, digestion efficiency, energy expenditure, and respiratory quotient using a novel isolator-housed metabolic cage system, which allows long-term measurements without contamination risk. This demonstrated that microbiota-released calories are perfectly balanced by decreased food intake in fully colonized versus gnotobiotic OligoMM12 and GF mice fed a standard chow diet, i.e., microbiota-released calories can in fact be well integrated into appetite control. We also observed no significant difference in energy expenditure after normalization by lean mass between the different microbiota groups, suggesting that cumulative small differences in energy balance, or altered energy storage, must underlie fat accumulation in OligoMM12 mice. Consistent with altered energy storage, major differences were observed in the type of respiratory substrates used in metabolism over the circadian cycle: In GF mice, the respiratory exchange ratio (RER) was consistently lower than that of fully colonized mice at all times of day, indicative of more reliance on fat and less on glucose metabolism. Intriguingly, the RER of OligoMM12-colonized gnotobiotic mice phenocopied fully colonized mice during the dark (active/eating) phase but phenocopied GF mice during the light (fasting/resting) phase. Further, OligoMM12-colonized mice showed a GF-like drop in liver glycogen storage during the light phase and both liver and plasma metabolomes of OligoMM12 mice clustered closely with GF mice. This implies the existence of microbiota functions that are required to maintain normal host metabolism during the resting/fasting phase of circadian cycle and which are absent in the OligoMM12 consortium.
P‐131: Polarization Independent and Fast Response Phase Modulators Using Orthogonally Orientated Liquid Crystal Gels (2006)

Abstract A polarization independent phase modulator using two ultra‐thin homogeneously stratified liquid crystal gels is demonstrated. In addition to the polarization independence and submillisecond response time, our liquid crystal gel possesses a much larger phase change and lower operating voltage than the nanosized polymer‐dispersed liquid crystal.
Micro‐Optics 3D Printed via Multi‐Photon Laser Lithography (Advanced Optical Materials 1/2023) (2023)

Multi-photon lithography is realized by a femtosecond laser direct writing in a photopolymer (see article number 2201701 by Carlo Liberale, Mangirdas Malinauskas, and co-workers). It is an ultra-precise optical 3D printing technique enabling additive manufacturing of free-form geometries. It is being established for rapid prototyping and production of miniature optical elements and stacked compound components: diffractive, refractive, guiding, filtering, polarizing, and many other optical functions can be merged into monolith devices with super-wavelength and sub-wavelength features. Recent advances are enabling creation of multi-functional devices out of diverse optical grade materials, including high refractive index, high damage threshold, and even glassy ones.
The clinical value of genetic analyses of bone and soft tissue tumors (2016)

Tumors of bone and soft tissue are common but only constitute 1 % of all malignant tumors. The malignant tumors are often difficult to diagnose due to their rarity and morphological resemblance between subtypes. This makes the diagnostic process challenging. Thus, there is a need for ancillary techniques, such as genetic analyses, not only for diagnostic purposes, but also for obtaining information that could be useful for treatment and prognosis. Different types of bone and soft tissue tumors, both benign and malignant, were analyzed. The tumor material used included needle aspiration biopsies, fresh and frozen surgical biopsies and formalin-fixed tissue. In paper I we compared karyotypes obtained by fine needle aspiration (FNA), core-needle (CNB) and surgical biospies. Chromosome banding analysis found clonal aberrations in 64% of surgical biopsies, in 48% of CNB and in 24% of FNA. These results suggest that chromosome banding analysis should be avoided on FNA and CNB. In paper II a pediatric giant fibroadenoma was analyzed with SNP array, revealing trisomies, uniparental isodisomy for chromosomes 10, 11 and 22 and a homozygous deletion of PARVA, indicating that SNP array provides information on pediatric breast tumors. In paper III we showed that the balanced translocation t(7;19)(q22;q13) results in a novel fusion gene SERPINE1-FOSB, which characterizes a malignant vascular tumor called pseudomyogenic hemangioendothelioma. The results were obtained by combining FISH, PCR and NGS-based RNA sequencing. In paper IV we successfully used RNA sequencing on formalin-fixed tissue to search for gene fusions in benign fibrous histiocytoma; a novel member of the protein kinase C family was shown to be involved. In paper V we studied pediatric rhabdomyosarcomas using mainly SNP array. We could show that this technique reveals many diagnostically and prognostically important aberrations, but that additional technologies for gene fusion detection must be employed. Thus, different genetic techniques provide different types of information, which must be taken into account when selecting method(s) for clinical, diagnostic purposes. None of the techniques used in the present studies is sufficient for detecting all clinically relevant genetic aberrations in bone and soft tissue tumors.
MicroRNA-124 Enhances Dopamine Receptor Expression and Neuronal Proliferation in Mouse Models of Parkinson’s Disease via the Hedgehog Signaling Pathway by Targeting EDN2 (2019)

Recent studies have elaborated on the concept that a number of microRNAs (miRNAs) have a potential effect on the pathogenesis and development of Parkinson's disease (PD). PD is recognized as a common progressive bradykinetic disorder that results from the death of dopaminergic neurons in the substantia nigra. The purpose of this study was to explore whether microRNA-124 (miR-124) affected dopamine receptor (DAR) expression and neuronal proliferation and apoptosis in the 1-methyl-4-pheny-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse models of PD. The targeting relationship of miR-124 and EDN2 was confirmed through bioinformatic predictions and dual-luciferase reporter assay. The expression of miR-124 and EDN2 was altered to assess their effect on the expression of DAR in the substantia nigra and isolated neurons, as well as the neuronal proliferation and apoptosis rate. The obtained results implied that the treatments of miR-124 mimic and si-EDN2 resulted in elevated expressions of Glil, SHH, PTCH1, DAT, DRD1, and DRD2. However, these treatments facilitated neuronal proliferation and suppressed neuronal apoptosis, corresponding to reduced expression of caspase-3 and Bax, as well as increased levels of Bcl-2 expression. These results were discovered to be achieved through the activation of the Hedgehog signaling pathway. With this taken into account, our study demonstrated that miR-124 overexpression promoted DAR expression and neuronal proliferation and suppressed neuronal apoptosis by downregulating EDN2 via activating the Hedgehog signaling pathway.
The laryngeal mask airway (1989)

A prototype size 3 laryngeal mask was used in 100 patients by 18 anaesthetists with no previous experience of its use. A clear and unobstructed airway was obtained in 98% of patients, without requiring support of the jaw, thus leaving the anaesthetists' hands entirely free. The patency of the airway did not deteriorate during the course of the anaesthetic. In 10 patients there was obstruction of the airway at the first attempt to place it without the introducer and this obstruction appeared to be as a result of downfolding of the epiglottis. Subsequent attempts at passage were successful in all 10 patients. The seal between the mask and the larynx was adequate for artificial ventilation of the patients, but the mean leak pressure was 1.7 kPa.
Leaching studies for the recovery of tin from the solder of waste printed circuit boards (2010)

Printed Circuit Boards (PCBs) are one of the important components of electrical and electronic equipments, which contain valuable, precious and hazardous metals besides the other materials such as plastic, glass etc. Large quantities of waste PCBs from different equipments are generated due to the replacement of old one with the launching of new and efficient models with advance features. The recycling of such waste materials is necessary to conserve the limited resources and also to protect the environment. Present paper is focused on the recovery of tin from solder material used in PCBs for fixing the various electronic components such as capacitor, resistor, connectors etc. Metals layers of PCBs are separated by swelling of the resin using organic solvent as an alternative traditional mechanical pre-treatment process. The main focus of the paper is the leaching of lead and tin from epoxy resin obtained after the liberation of thin metal sheet from organic swelled PCBs. Therefore, the leaching studies were carried out with pure tin metal and solder materials (52.6 % Sn and balance Pb) under varying hydrochloric acid concentration, temperature at fixed pulp density 10 g/L. The experimental data indicated that the 88.1% pure tin was dissolved with 9M HCl at 90°C within leaching time 1hr 15 min, however percentage dissolution was found to increase up to 98% with increase in leaching time to 2 hrs 45 min. The dissolution of tin from the solder was found to be 99.99% with 5M HCl at 90°C in 1hr 15 min. The kinetics of leaching of tin from solder was studied in hydrochloric acid. Leaching reaction followed “film diffusion control dense shrinking sphere model” with rate equation 1–(1–X)2/3 = Kct. The optimized condition obtained from these studies will be useful for the removal of tin from solder material of waste PCBs and lead metal remained in the residue could be leached out by nitric acid for safe disposal or utilization of resin residue to the environment.
REDUCING ENVIRONMENTAL EMISSIONS IN TANNERIES (2002)

Tanning, in particular chrome leather production, is still characterised by an inefficient use of raw material and the production of highly polluted wastewater and solid wastes. A part of the emissions can be prevented by introducing clean tanning technologies, the remaining emissions can be treated. Clean production technologies and waste (water) treatment technologies should have a designed complimentarity. Anaerobic wastewater treatment with recovery of sulfides, sulfur and energy (biogas) is a cornerstone in such integral clean chrome leather technology.
Higher Yielding Isolation of Kinsenoside in Anoectochilus and Its Antihyperliposis Effect. (2001)

A higher concentration of kinsenoside, 3-(R)-3-beta-D-glucopyranosyloxybutanolide (1), was detected in the crude drug Anoectochilusformosanus, and A. koshunensis by HPLC analysis. A methylation reaction occurred to give methyl ester (4) when the lactone ring of 1 was cleaved by silica gel catalysis using methanol containing solvent used in the purification step resulting in difficulty to purify 1. To avoid the cleavage reaction, a reversed-phase or silica gel column without methanol was used to give a high yield of 1. In an anti-hyperliposis assay using high-fat diet rats, 1 significantly reduced the weights of body and liver, and also decreased the triglyceride level in the liver compared to those of control rats. On the other hand, the epimer of 1, 3-(S)-3-beta-glucopyranosy-loxybutanolide (2), trivially named goodyeroside A, which was isolated from Goodyera species, had no effect for anti-hyperliposis. In aurothioglucose-induced obese mouse, 1 suppressed the body and liver weight increase, significantly ameliorated the triglyceride level in the liver, and also reduced the deposition of uterine fat-pads.
Thymoglobulin induction and steroid avoidance in cardiac transplantation: results of a prospective, randomized, controlled study (2007)

CS-avoidance regimen with Thymoglobulin induction appeared to be safe and effective in cardiac transplantation. Further studies are required to demonstrate the long-term safety and benefits of such a regimen.
Exocytosis of Mesoporous Silica Nanoparticles from Mammalian Cells: From Asymmetric Cell‐to‐Cell Transfer to Protein Harvesting (2011)

The exocytosis of mesoporous silica nanoparticles (MSNs) from mammalian cells is demonstrated for the first time. The differences in the degree of exocytosis of MSNs between healthy and cancer cells are shown to be responsible for the asymmetric transfer of the particles between both cell types. The exo­cytosis of highly adsorbent magnetic MSNs proves to be useful as a means for harvesting biomolecules from living cells. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Inverse design of proteins with hydrophobic and polar amino acids (1997)

A two amino acid (hydrophobic and polar) scheme is used to perform the design on target conformations corresponding to the native states of twenty single chain proteins. Strikingly, the percentage of successful identification of the nature of the residues benchmarked against naturally occurring proteins and their homologues is around 75 % independent of the complexity of the design procedure. Typically, the lowest success rate occurs for residues such as alanine that have a high secondary structure functionality. Using a simple lattice model, we argue that one possible shortcoming of the model studied may involve the coarse-graining of the twenty kinds of amino acids into just two effective types.
Common variants of NRXN1, LRP1B and RORA are associated with increased ventricular volumes in psychosis - GWAS findings from the B-SNIP deep phenotyping study (2017)

ABSTRACT Schizophrenia, Schizoaffective, and Bipolar Disorders share common illness traits, intermediate phenotypes and a partially overlapping polygenic basis. We performed GWAS on deep phenotyping data, including structural MRI and DTI, clinical, and behavioral scales from 1,115 cases and controls. Significant associations were observed with two cerebrospinal fluid volumes: the temporal horn of left lateral ventricle was associated with NRXN1 , and the volume of the cavum septum pellucidum was associated with LRP1B and RORA . Both volumes were associated with illness. Suggestive associations were observed with local gyrification indices, fractional anisotropy and age at onset. The deep phenotyping approach allowed unexpected genetic sharing to be found between phenotypes, including temporal horn of left lateral ventricle and age at onset.
Quantum computation by measurements (2003)

We first consider various methods for the indirect implementation of unitary gates. We apply these methods to rederive the universality of 4-qubit measurements based on a scheme much simpler than Nielsen's original construction [quant-ph/0108020]. Then, we prove the universality of simple discrete sets of 2-qubit measurements, again using a scheme simplifying the initial construction [quant-ph/0111122]. Finally, we show how to use a single 4-qubit measurement to achieve universal quantum computation, and outline a proof for the universality of almost all maximally entangling 4-qubit measurements.
Language pattern analysis for automotive natural language speech applications (2010)

Natural language speech user interfaces offer a compelling choice of user interaction for the automotive market. With the increasing number of domains in which speech applications are applied, drivers must currently memorize many command words to control traditional speech interfaces. In contrast, natural language interfaces demand only a basic understanding of the system model instead of memorizing keywords and predefined patterns. To utilize natural language interfaces optimally, designers need to better comprehend how people utter their requests to express their intentions. In this study, we collected a corpus of utterances from users who interacted freely with an automotive natural language speech application. We analyzed the corpus by employing a corpus linguistic technique. As a result, natural language utterances can be classified into three components: information data, context relevant words, and non context relevant vocabulary. Applying this classification, users tended to repeat similar utterance patterns composed from a very limited set of different words. Most of the vocabulary in longer utterances was found to be non context restrictive providing no information. Moreover, users could be distinguished by their language patterns. Finally, this information can be used for the development of natural language speech applications. Some initial ideas are discussed in the paper.
Direct Access to Titanocene Imides via Bis(η5:η1-penta-fulvene)titanium Complexes and Primary Amines (2018)

The formation of the titanocene imido complexes 2b, 4, and 5 via double N–H bond activations at ambient temperature of sterically demanding amines (2,6-diisopropylaniline, tert-butylamine) by the use of the bis(η5:η1-adamantylidenepentafulvene)titanium complex (1) has been investigated. The titanium imido complex 2b exists in equilibrium with its corresponding titanium monoamide complex 2a. The equilibrium can be shifted to the side of the imide 2b by increasing the temperature. Starting from the equilibrium 2a/2b, or the titanium imido pyridine adduct 5, a broad range of [2 + 2] cycloaddition reactions are realized. In reactions with alkynes, the regioselective formation of the azacyclobutenes 6 and 7 are observed. By using carbodiimides, asymmetric (8 and 10a) and symmetric cycloaddition products (9 and 10b) are formed. In the reaction with isocyanates, dependent on the substitution pattern of the Ti═NR imido unit, the C═O or the C═N [2 + 2] cycloaddition occurs, resulting in the N,O-bound ureato(2-) complex 11 or the N,N-bound ureato(2-) complex 13. In the presence of isocyanates and nitriles, the equilibrium 2a/2b results in ring enlargement reactions to six-membered rings (12, 14) by insertion of a second equivalent of the substrate into the Ti–N bonds.
Dehalogenation and biodegradation of brominated phenols and benzoic acids under iron-reducing, sulfidogenic, and methanogenic conditions (1997)

The anaerobic biodegradation of monobrominated phenols and benzoic acids by microorganisms enriched from marine and estuarine sediments was determined in the presence of different electron acceptors [i.e., Fe(III), SO4(2-), or HCO3-]. Under all conditions tested, the bromophenol isomers were utilized without a lengthy lag period whereas the bromobenzoate isomers were utilized only after a lag period of 23 to 64 days. 2-Bromophenol was debrominated to phenol, with the subsequent utilization of phenol under all three reducing conditions. Debromination of 3-bromophenol and 4-bromophenol was also observed under sulfidogenic and methanogenic conditions but not under iron-reducing conditions. In the bromobenzoate-degrading cultures, no intermediates were observed under any of the conditions tested. Debromination rates were higher under methanogenic conditions than under sulfate-reducing or iron-reducing conditions. The stoichiometric reduction of sulfate or Fe(III) and the utilization of bromophenols and phenol indicated that biodegradation was coupled to sulfate or iron reduction, respectively. The production of phenol as a transient intermediate demonstrates that reductive dehalogenation is the initial step in the biodegradation of bromophenols under iron- and sulfate-reducing conditions.
Low-Complexity EM-based Joint Acquisition of the Carrier Frequency Offset and IQ Imbalance (2008)

New air interfaces are currently being developed to meet the high spectral efficiency requirements of the emerging wireless communication systems. In this context, OFDM is considered as a promising air interface candidate for both indoor and outdoor communications. Besides spectral efficiency and power consumption, the production cost of the transceiver should also be optimized. Direct-conversion radio frequency receivers are appealing because they avoid costly intermediate frequency hardware. However, they imply analog IQ separation, introducing a phase and amplitude mismatch between the I and Q branches. A communication system based on OFDM is sensitive to synchronization errors, such as CFO, and to front- end non-idealities, such as IQ imbalance. The goal of this paper is to use the iterative EM algorithm to acquire jointly the CFO and the IQ imbalance. The solution relies on a standard compliant repetitive preamble and does not require the knowledge of the propagation channel. Based on a second order approximation of the likelihood function, the complexity of the EM algorithm is significantly reduced. The algorithm is shown to perform extremely well: the estimates of the CFO and of the IQ imbalance converge to their ML estimate after less than 3 iterations. It outperforms state-of-the-art solutions significantly and suffers from a lower computational complexity. While the CFO estimate is robust against variations of the SNR, the IQ imbalance estimate accuracy is reduced at values of the SNR below 10 dB and above 35 dB.