Miracle-dz/UniFAR-FTUs huggingface dataset:
Marginally hydrophobic transmembrane α‐helices shaping membrane protein folding

Cells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices—implying a dynamic relationship between membrane proteins and their environment.
Estimating performance from capabilities in business process improvement

The research indicates there is a positive link between the improvement capability of an organisation and the intensity of effort applied to a business process improvement (BPI) project or initiative. While a degree of stochastic variation in applied effort to any particular improvement project may be expected there is a clear need to quantify the causal relationship, to assist management decision, and to enhance the chance of achieving and sustaining the expected improvement targets. The paper aims to discuss these issues. ,The paper presents a method to obtain the function that estimates the range of applicable effort an organisation can expect to be able to apply based on their current improvement capability. The method used analysed published data as well as regression analysis of new data points obtained from completed process improvement projects. ,The level of effort available to be applied to a process improvement project can be expressed as a regression function expressing the possible range of achievable BPI performance within 90 per cent confidence limits. ,The data set applied by this research is limited due to constraints during the research project. A more accurate function can be obtained with more industry data. ,When the described function is combined with a separate non-linear function of performance gain vs effort a model of performance gain for a process improvement project as a function of organisational improvement capability is obtained. The probability of success in achieving performance targets may be estimated for a process improvement project. ,The method developed in this research is novel and unique and has the potential to be applied to assessing an organisation’s capability to manage change.
Bendable ITO-free Organic Solar Cells with Highly Conductive and Flexible PEDOT:PSS Electrodes on Plastic Substrates.

UNLABELLED Flexible and transparent electrodes have great potential for photon transmission and charge-carrier collection for next generation electronics compared to rigid electronics with indium tin oxide (ITO)-coated glass substrates. This study describes a comprehensive study of the electrical, morphological, optical, structural, and mechanical properties of poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) ( PEDOT PSS) films treated by methanol and methanesulfonic acid (MSA), which are coated on hydrophobic flexible plastic substrates. Such a film coated on hydrophobic plastic substrates exhibits a high conductivity up to 3560 S cm(-1) and a good mechanical flexibility. Moreover, the use of the films to fabricate bendable ITO-free organic solar cells (OSCs) integrated on plastic substrates was presented. The bendable devices based on P3HT:PCBM not only exhibit a high power conversion efficiency (PCE) up to 3.92%, which is comparable to 4.30% of the rigid devices with ITO-coated glass substrates, but also keep about 80% in PCE of the initial value after 100 time bending with a bending radius of 14 mm in the ambient atmosphere. This work provides a novel route to dramatically improve the conductivity of PEDOT PSS electrodes, as well as the mechanical flexibility of highly efficient organic electronics with the flexible electrodes.
Structure–function correlations in tyrosinases

Tyrosinases are metalloenzymes belonging to the type‐3 copper protein family which contain two copper ions in the active site. They are found in various prokaryotes as well as in plants, fungi, arthropods, and mammals and are responsible for pigmentation, wound healing, radiation protection, and primary immune response. Tyrosinases perform two sequential enzymatic reactions: hydroxylation of monophenols and oxidation of diphenols to form quinones which polymerize spontaneously to melanin. Two other members of this family are catechol oxidases, which are prevalent mainly in plants and perform only the second oxidation step, and hemocyanins, which lack enzymatic activity and are oxygen carriers. In the last decade, several structures of plant and bacterial tyrosinases were determined, some with substrates or inhibitors, highlighting features and residues which are important for copper uptake and catalysis. This review summarizes the updated information on structure–function correlations in tyrosinases along with comparison to other type‐3 copper proteins.
A Study of the Pharmacist-Patient Relationship: Covenant or Contract?

ABSTRACTThis national study was designed to identify the nature of the pharmacist-patient relationship by examining the attitudes of pharmacists. It was also designed to determine whether these attitudes were covenant or contract based and how demographic or situational variables contributed to these attitudes. The data concerning the pharmacists' attitudes were collected using a mail survey. Analysis of the data revealed that there were seven underlying dimensions to die pharmacists' attitudes toward the pharmacist-patient relationship. Pharmacists' relationships with patients seemed to rely heavily on practice motive and commitment to patients. Also, the covenant attitude seemed to increase as the pharmacists' education increased and as the work setting became more clinical. These conclusions are important in light of the American Pharmaceutical Association recommendation that pharmacists have a covenant-type relationship with patients.
Bounds on the extreme eigenvalues of positive-definite Toeplitz matrices

Easily computable bounds on the extreme eigenvalues of positive semidefinite (PSD) Toeplitz matrices are presented. The bounds are especially suitable for matrices of relatively small dimension. The bounds are derived for the wider class of PSD Hermitian matrices and interpreted via the Levinson-Durbin Algorithm for Toeplitz matrices. As a by-product of this derivation an order-recursive algorithm for the eigenvector/eigenvalue decomposition is obtained, and certain properties of the eigenvalues distribution are revealed. >
A Multi-Level Dimension Reduction Monte-Carlo Method for Jump-Diffusion Models

This paper develops and analyses convergence properties of a novel multi-level Monte-Carlo (mlMC) method for computing prices and hedging parameters of plain-vanilla European options under a very general $b$-dimensional jump-diffusion model, where $b$ is arbitrary.The model includes stochastic variance and multi-factor Gaussian interest short rate(s). The proposed mlMC method is built upon (i) the powerful dimension and variance reduction approach developed in Dang et. al 2015 for jump-diffusion models, which, for certain jump distributions, reduces the dimensions of the problem from $b$ to $1$, namely the variance factor, and (ii) the highly effective multi-level MC approach of Giles 2008 applied to that factor. As a result, the proposed multi-level approach avoids potential difficulties associated with the standard multi-level approach in effectively handling simultaneously both multi-dimensionality and jumps. Numerical analysis shows that, when a time discretization scheme having first-order strong convergence, such as the Lamperti-Backward-Euler or Milstein schemes, is used in Step (ii), the proposed MC method requires only an overall complexity $\mathcal{O}(\epsilon^{-2})$ to achieve a root-mean-square error of $\epsilon$. Numerical results illustrating the convergence properties and efficiency of the method with jump sizes following normal and double-exponential distributions are presented.
The rates of Assignment of Thesaurus Terms in the Eric Information Retrieval System: an Analysis of Hierarchies and Levels

The study examined the rates of use of descriptors in the ERIC system during 1966–1986 to determine if certain levels of terms were used more than others and if patterns of use were similar among hierarchies in the ERIC Thesaurus. The postings per document measure indicated how often a term had been assigned to documents during its life. This was averaged for each level in the 252 multilevel hierarchies. With little exception there was not much variation in postings per document among levels nor among hierarchies. The major exception was the mean rate of 725 postings per 100,000 documents for the broadest terms in the twenty‐nine hierarchies having four levels each. This rate was significantly higher than for the narrowest levels in these hierarchies. The lack of variation in most hierarchies suggests that all terms currently in the system are important and used by indexers. Searchers should be aware of the power of the broadest terms.
Intraoperative Ultrasonography During Transoral Robotic Surgery

Objective: This study describes the potential application of intraoperative ultrasound imaging during transoral robotic surgery (TORS). Methods: Ultrasound imaging was performed during transoral robotic resection of oropharyngeal tumors in 10 patients at a tertiary academic center. Ultrasound imaging was utilized to identify large-caliber vessels adjacent to the surgical site. Measurements were also taken on the ultrasound of tumor thickness to determine the deep margin. Following resection, the tumor was sectioned, and a gross measurement of the tumor thickness was obtained. Results: Intraoperative ultrasound use led to the identification of larger-caliber blood vessels within the operative field prior to encountering them visually. Ultrasound could also aid in defining deep tumor margins; the tumor thickness measured via ultrasound was found to be accurate within 1 to 2 mm of the grossly measured tumor thickness. This allowed for focused, careful dissection to protect and avoid blood vessels during dissection as well as improved tumor resection. Conclusions: The use of intraoperative ultrasound provides additional information to the head and neck surgeon during TORS. This may be used to identify blood vessels and assess tumor margins, thereby improving the safety and efficacy of TORS.
Outcomes of Laryngeal Reinnervation for Unilateral Vocal Fold Paralysis in Children

Objective: Outcomes of laryngeal reinnervation with ansa-cervicalis for unilateral vocal fold paralysis (UVFP) may be influenced by age of the patient and time interval between laryngeal nerve injury and reinnervation, suggesting less favorable outcomes in older patients and greater than 2-year time interval after injury. This study examines these issues in the pediatric population. Method: Review of prospectively collected data set of 35 children and adolescents (1-21 years) that underwent ansa-recurrent laryngeal nerve (RLN) laryngeal reinnervation for UVFP. Results: The time from RLN injury to reinnervation averaged 5.0 years (range, 0.8-15.2 years). No correlation was found between age at reinnervation (r = 0.15) and patient- or parent-reported global percentage voice outcome or perceptual ratings. There was slight negative correlation in duration between RLN injury and reinnervation and voice outcomes (r = −0.31). Postoperative voice self/surrogate global percentage rating average was 80.5% (range, 50%-100%), and perceptual rating GRBAS sum score average was 2.9 (range, 0-7). Conclusion: In pediatric ansa-RLN reinnervation for UVFP, no correlation between age at surgery and postoperative outcome was found. Denervation duration showed slight negative correlation, similar to what has been reported in adults, though voice improvement was seen in all patients.
Revisiting Place-Pitch Match in CI Recipients Using 3D Imaging Analysis

Objective: To improve the estimation of the perceived pitch in a single-sided deaf cochlear implant (CI) listener by using accurate 3-dimensional (3D) image analysis of the cochlear electrode positions together with the predicted tonotopical function for humans. Methods: An SSD CI user underwent a Cone-Beam computed tomography (CBCT) scan. Electrode contacts were marked in 3D space in relation to the nearest point on the cochlear lateral wall. Distance to the base of the lateral wall was calculated and plotted against the place-pitch function for humans. An adaptive procedure was used to elicit the perceived pitch of electrically evoked stimulation by matching it with a contralateral acoustic pitch. Results: The electrically evoked pitch percept matched well with the calculated frequency. The median mismatch in octaves was 0.12 for our method in comparison to 0.69 using the conventional Stenvers view. Conclusion: A method of improved image analysis is described that can be used to predict the pitch percept on corresponding cochlear electrode positions. This method shows the potential of 3D imaging in CI fitting optimization.
A multispecific monoclonal antibody G2 recognizes at least three completely different epitope sequences with high affinity

A monoclonal antibody (mAb) G2 possesses an unusual characteristic of reacting with at least three proteins (ATP6V1C1, SEPT3, and C6H10orf76) other than its original antigen, chicken prion protein (ChPrP). The epitopes on ChPrP and ATP6V1C1 have been identified previously. In this study, we identified the epitope in the third protein, SEPT3. Interestingly, there was no amino acid sequence similarity among the epitopes on the three proteins. These epitopes had high binding affinities to G2 (KD = ∼10−7 M for monovalent binding and KD = ∼10−9 M for divalent binding), as determined using a SPR biosensor. This is the first report on a three‐in‐one mAb recognizing completely different epitope sequences with high affinity. Additionally, competitive ELISA indicated that the binding sites on G2, specific for the three different epitopes, overlapped, suggesting that the antigen‐binding site may be flexible in the free form and capable of adapting to at least three different conformations to enable interactions with three different antigens.
The structure of glucose‐1‐phosphate thymidylyltransferase from Mycobacterium tuberculosis reveals the location of an essential magnesium ion in the RmlA‐type enzymes

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, continues to be a major threat to populations worldwide. Whereas the disease is treatable, the drug regimen is arduous at best with the use of four antimicrobials over a six‐month period. There is clearly a pressing need for the development of new therapeutics. One potential target for structure‐based drug design is the enzyme RmlA, a glucose‐1‐phosphate thymidylyltransferase. This enzyme catalyzes the first step in the biosynthesis of l‐rhamnose, which is a deoxysugar critical for the integrity of the bacterium's cell wall. Here, we report the X‐ray structures of M. tuberculosis RmlA in complex with either dTTP or dTDP‐glucose to 1.6 Å and 1.85 Å resolution, respectively. In the RmlA/dTTP complex, two magnesium ions were observed binding to the nucleotide, both ligated in octahedral coordination spheres. In the RmlA/dTDP‐glucose complex, only a single magnesium ion was observed. Importantly, for RmlA‐type enzymes with known three‐dimensional structures, not one model shows the position of the magnesium ion bound to the nucleotide‐linked sugar. As such, this investigation represents the first direct observation of the manner in which a magnesium ion is coordinated to the RmlA product and thus has important ramifications for structure‐based drug design. In the past, molecular modeling procedures have been employed to derive a three‐dimensional model of the M. tuberculosis RmlA for drug design. The X‐ray structures presented herein provide a superior molecular scaffold for such endeavors in the treatment of one of the world's deadliest diseases.
Expert system for automatically correcting OCR output

This paper describes a new expert system for automatically correcting errors made by optical character recognition (OCR) devices. The system, which we call the post-processing system, is designed to improve the quality of text produced by an OCR device in preparation for subsequent retrieval from an information system. The system is composed of numerous parts: an information retrieval system, an English dictionary, a domain-specific dictionary, and a collection of algorithms and heuristics designed to correct as many OCR errors as possible. For the remaining errors that cannot be corrected, the system passes them on to a user-level editing program. This post-processing system can be viewed as part of a larger system that would streamline the steps of taking a document from its hard copy form to its usable electronic form, or it can be considered a stand alone system for OCR error correction. An earlier version of this system has been used to process approximately 10,000 pages of OCR generated text. Among the OCR errors discovered by this version, about 87% were corrected. We implement numerous new parts of the system, test this new version, and present the results.
Seeking out collective wisdom: cataloguers' use of social media

Purpose – The purpose of this paper is to explore the frequency with which Internet-based social media (namely, wikis, blogs, forums and electronic mailing lists) are used by cataloguers to seek what Judith Hopkins (2002) defines as “specific (and immediate) current awareness” and “general current awareness”. The aim is to provide some insight into whether social media play a part in day-to-day practice and on-the-job learning of cataloguers. Design/methodology/approach – A survey research was conducted. An online questionnaire was made available to self-selecting respondents via electronic mailing lists (AUTOCAT, CatSIG listserv, NZLibs listserv) and 176 responses were received. Findings – The study found that general current awareness information was more frequently sought via Internet-based social media than specific (and immediate) current awareness. A statistically significant, weak positive correlation was found between the variables of “number of cataloguers working in an organization” and “frequen.
Investigating the Structural Change in Protein Aqueous Solution Using Temperature-Dependent Near-Infrared Spectroscopy and Continuous Wavelet Transform

The circulatory protein, human serum albumin (HSA), is widely used as a model protein for the study of protein structure. In this work, the structures of human serum albumin in aqueous solutions are studied using temperature-dependent near-infrared (NIR) spectroscopy with the aid of continuous wavelet transform (CWT). Near-infrared spectra of human serum albumin solutions with different concentrations were measured over a temperature range of 30–85 ℃. Then, continuous wavelet transform was performed on the spectra to enhance the resolution. As a result of the resolution enhancement, spectral bands around 4361, 4521, 4600 and 4260 cm−1 were extracted from the overlapping low-resolution signals. The four bands can be assigned to the protein structures of α-helix, β-sheet, an intermediate state and side chains, respectively. The variations in intensity of the bands around 4361 and 4521 cm−1 with temperature show that the increase of temperature leads to the loss of α-helical structure but the formation of β-sheet, and the denaturation temperature of human serum albumin is about 55 ℃. The variation of the band around 4600 cm−1 indicates that the temperature-induced unfolding process of human serum albumin occurs through a stable intermediate state, and a significant change in the microenvironment of the side chains about 63 ℃ is observed from the variation of the band around 4260 cm−1. On the other hand, the transformed spectra in the region of 8000–5600 cm−1 provide an explicit evidence for the structural changes of water during the process of protein denaturation, and the unfolding process of HSA can be reflected by these changes.
Broadband Infrared Spectroscopy for Non-Contact Measurement of Neurological Disease Biomarkers in Cerebrospinal Fluid

Cerebrospinal fluid (CSF) is a clear and colorless biological fluid which circulates within brain ventricles (cavities), the spinal cord’s central canal, the space between the brain and the spinal cord, as well as their protective coverings, the meninges. Cerebrospinal fluid contains different constituents, such as albumin and lactate, whose levels are used clinically as biomarkers of neurodegenerative disorders. In current clinical practice, analysis of CSF content for the diagnosis of central nervous system disorders requires an invasive procedure known as lumbar puncture or spinal tap. With the aim of developing a noninvasive alternative, we report here the spectral behavior of albumin and lactate over a broad wavelength range of 600–2000 nm, after each was added separately at varying normal and abnormal concentration levels to artificial CSF (aCSF). Spectral measurements were conducted simultaneously by two different spectrometers working at different spectral ranges in transmittance mode. Spectral analysis revealed that albumin and lactate each possesses its own first and second derivative absorbance spectra fingerprint between 1660 and 1810 nm. Distinguishing albumin from lactate by their spectral data enabled the differentiation between aCSF conditions modeling different neurological disorders. Spectral changes of each compound strongly correlated (R2 > 0.9) with absorbance derivative spectra peaks at specific wavelengths, when analyzed by linear regression with variations in their concentration. These findings suggest the feasibility of CSF biomarker assessment by broadband infrared spectroscopy.
AIR POLLUTION AND DAILY MORTALITY

Statistical manipulation of environmental and mortality data for LA County (1956-58) showed distinct seasonal patterns which, when eliminated by harmonic analysis, revealed no influence of air pollution on daily mortality. This report emphasizes that daily mortality is at best a crude estimate of environmental effects since it depends so much on bodily resistance to cumulative stress.