Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme

To further investigate the ways in which proteins respond to changes in the length of the polypeptide chain, a series of 32 insertions and five deletions were made within nine different α‐helices of T4 lysozyme. In most cases, the inserted amino acid was a single alanine, although in some instances up to four residues, not necessarily alanine, were used. Different insertions destabilized the protein by different amounts, ranging from approximately 1 to 6 kcal/mol. In one case, no protein could be obtained. An “extension” mutant in which the carboxy terminus of the molecule was extended by four alanines increased stability by 0.3 kcal/mol. For the deletions, the loss in stability ranged from approximately 3 to 5 kcal/mol. The structures of six insertion mutants, as well as one deletion mutant and the extension mutant, were determined, three in crystal forms nonisomorphous with wild type. In all cases, including previously described insertion mutants within a single α‐helix, there appears to be a strong tendency to preserve the helix by translocating residues so that the effects of the insertion are propagated into a bend or loop at one end or the other of the helix. In three mutants, even the hydrophobic core was disrupted so as to permit the preservation of the α‐helix containing the insertion. Translocation (or “register shift”) was also observed for the deletion mutant, in this case a loop at the end of the helix being shortened. In general, when translocation occurs, the reduction in stability is only moderate, averaging 2.5 kcal/mol. Only in the most extreme cases does “bulging” or “looping‐out” occur within the body of an α‐helix, in which case the destabilization is substantial, averaging 4.9 kcal/mol. Looping‐out can occur for insertions close to the end of a helix, in which case the destabilization is less severe, averaging 2.6 kcal/mol. Mutant A73‐[AAA], as well as mutants R119‐[A] and V131‐[A], include shifts in the backbone of 3–6 Å, extending over 20 residues or more. As a result, residues 114–142, which form a “cap” on the carboxy‐terminal domain, undergo substantial reorganizations such that the interface between this “cap” and the rest of the protein is altered substantially. In the case of mutant A73‐[AAA], two nearby α‐helices, which form a bend of approximately 105 degrees in the wild‐type structure, reorganize in the mutant structure to form a single, essentially straight helix. These structural responses to mutation demonstrate the plasticity of protein structures and illustrate ways in which their three‐dimensional structures might change during evolution.
A 312-GHz CMOS Injection-Locked Radiator With Chip-and-Package Distributed Antenna

This paper presents an injected-locked THz radiator integrating a half-quadrature voltage-controlled oscillator (HQVCO), four injection-locked frequency quadruplers (ILFQs), and a chip-and-package distributed antenna (DA). At the system level, an architecture based on injection locking is employed to allow individual optimization of the output power and the phase noise. At the circuit level, intrinsic-delay compensation and harmonic boosting techniques are proposed to optimize the phase noise of the HQVCO and the output power of the ILFQs, respectively. The proposed DA composed of four exciting elements on silicon chip and a primary radiator in low-temperature co-fired ceramic (LTCC) package features a wide bandwidth of 13% and a gain of 3.8 dBi without using lens at 312 GHz. Implemented in a 65-nm CMOS process, the radiator system occupying a core area of 0.36 mm2 achieves output frequency from 311.6 to 315.5 GHz and maximum equivalent isotropically radiated power (EIRP) of 10.5 dBm while consuming 300 mW. The output phase noise measures −109.3 dBc/Hz at 10-MHz offset and the dc-to-THz efficiency is 0.42%.
Complex of urokinase‐type plasminogen activator with its type 1 inhibitor predicts poor outcome in 576 patients with lymph node–negative breast carcinoma

The ability of a solid tumor to grow and metastasize has a significant dependence on protease systems, such as the plasminogen activation system. The plasminogen activation system includes the urokinase‐type plasminogen activator (uPA) and plasminogen activator inhibitor type 1 (PAI‐1), among other molecules. Both uPA and PAI‐1 are established prognostic factors for patients with breast carcinoma. In the current study, the authors investigated whether the complex of uPA with PAI‐1 is also associated with the natural course of this malignancy.
Uses and Abuses of Socio-Legal Studies

Many scholars have developed maps of impact and periodization of ideas and eras in the last fifty years of the socio-legal field. More recently other fields (e.g. behavioral economics) have both used and co-opted basic concepts and studies of the older socio-legal field (e.g. group behavior in corporate governance and social influences in decision making). Yet, judges, legal policy makers, and other actors in legal institutions continue to make, interpret, enforce and evaluate laws, often with empirical claims of validity or prediction, without actually referring to verifiable data or empirically valid patterns of social data. This chapter reviews, both through my own socio-legal work, and that of other scholars, the uses and abuses (or failure to use) socio-legal research (both empirical and conceptual) in law (doctrine, policy and theory). This essay describes the field’s and my own “origin” stories, rooted in key socio-legal ideas of law in social context, legal realism, legal pluralism, legal movements and institutions, “gaps” in the law on the books vs. the law in action, law and culture, legal theory, ideology and the role of law in social change. I then review some examples of “good” uses of socio-legal studies methods and theories (e.g. robust concepts and research findings on legal process, decision-making, enforcement of law and social control, and cultural meanings of law for lay people, as well as professionals), as well as some examples of misuses (or lack of use) of rigorous socio-legal studies. I conclude with some observations about why socio-legal studies remains somewhat marginalized in legal decision making (different “standards of proof” in different disciplines) and legal study generally (at both educational and research levels).
Lymphoid enhancer factor interacts with GATA‐3 and controls its function in T helper type 2 cells

GATA‐3 is the master transcription factor for T helper 2 (Th2) cell differentiation and is critical for the expression of Th2 cytokines. Little is known, however, about the nature of the functional molecular complexes of GATA‐3. We identified a high‐mobility group (HMG)‐box type transcription factor, lymphoid enhancer factor 1 (LEF‐1), in the GATA‐3 complex present in Th2 cells using a Flag‐calmodulin‐binding peptide (CBP)‐tag based proteomics method. The interaction between GATA‐3 and LEF‐1 was confirmed by co‐immunoprecipitation experiments using LEF‐1‐introduced T‐cell lineage TG40 cells. The HMG‐box domain of LEF‐1 and two zinc finger domains of GATA‐3 were found to be important for the physical association. The introduction of LEF‐1 into developing Th2 cells resulted in the suppression of Th2 cytokine production. The suppression was significantly lower in the cells into which a HMG‐box‐deleted LEF‐1 mutant was introduced. Moreover, LEF‐1 inhibited the binding activity of GATA‐3 to the interleukin (IL)‐5 promoter. These results suggest that LEF‐1 is involved in the GATA‐3 complex, while also regulating the GATA‐3 function, such as the induction of Th2 cytokine expression via the inhibition of the DNA‐binding activity of GATA‐3.
Comparison of causes of death using HEMO Study and HCFA end-stage renal disease death notification classification systems. The National Institutes of Health-funded Hemodialysis. Health Care Financing Administration.

Few data are available on the accuracy of death classification in patients with end-stage renal disease (ESRD). The National Institutes of Health-funded Hemodialysis (HEMO) Study allows the opportunity to compare cause of death recorded on the Health Care Financing Administration (HCFA) Death Notification Form 2746 with death classified by the HEMO Study. The HEMO Study cause of death is determined by trained HEMO Study Outcome Review Committee physicians. In this interim analysis, there were 220 deaths coded by both classification systems. Using the HEMO Study classification system, the most common cause of death was ischemic heart disease (20.4%), followed by arrhythmia and conduction problems (10.4%), cerebrovascular disease (8.6%), and non-access-related infections (7.7%). Using the HEMO Study final death classification as the reference standard, most differences in the two classification systems were related to coding of heart disease. Sensitivity for the HCFA classification ranged from 9.1% for congestive heart failure to 91.7% for malignancy, whereas specificity values were all greater than 78%. Positive predictive values ranged from 11.8% for other heart disease and conditions to 100% for malignancy and hepatobiliary disease, whereas negative predictive values were all greater than 85%. The kappa statistic between the two death classification systems ranged from 0.12 for congestive heart failure to 0.95 for malignancy. Studies using death classification from the HCFA ESRD death notification form for deaths secondary to either cardiovascular diseases or unknown causes should be interpreted cautiously.
On The Exact Security of Message Authentication Using Pseudorandom Functions

Traditionally, modes of Message Authentication Codes(MAC) such as Cipher Block Chaining (CBC) are instantiated using block ciphers or keyed Pseudo Random Permutations(PRP). However, one can also use domain preserving keyed Pseudo Random Functions(PRF) to instantiate MAC modes. The very first security proof of CBC-MAC [BKR00], essentially modeled the PRP as a PRF. Until now very little work has been done to investigate the difference between PRP vs PRF instantiations. Only known result is the rather loose folklore PRP-PRF transition of any PRP based security proof, which looses a factor of Ο ( σ 2 / 2 n ) (domain of PRF/PRP is {0, 1} n and adversary makes σ many PRP/PRF calls in total). This loss is significant, considering the fact tight Θ ( q 2 / 2 n ) security bounds have been known for PRP based EMAC and ECBC constructions (where q is the total number of adversary queries). In this work, we show for many variations of encrypted CBC MACs (i.e. EMAC, ECBC, FCBC, XCBC and TCBC), random function based instantiation has a security bound Ο ( q σ / 2 n ). This is a significant improvement over the folklore PRP/PRF transition. We also show this bound is optimal by providing an attack against the underlying PRF based CBC construction. This shows for EMAC, ECBC and FCBC, PRP instantiations are substantially more secure than PRF instantiations. Where as, for XCBC and TMAC, PRP instantiations are at least as secure as PRF instantiations.
Analysis of the Relationship Between GDP and FDI on the Economic Growth of Laos

In the current globalization stream, the foreign investment is an important role not only for developed country but at all especially the least developing country as Laos. This study aims to examine the relationship between the gross domestic product (GDP) and foreign direct investment (FDI) on economic growth of Laos by using data from 1985 to 2014. The long run relationship was analyzed by Johansen co-integration test and estimated the speed of adjustment by Vector Error Correction approach. Estimated results indicated that there was long run relationship running from FDI to GDP and the relation would return to the equilibrium in about 19 when it occurred. This study suggests that policy maker should improve the other factor for motivated FDI and accelerate Lao economy. This study examines the relationship between FDI and GDP of Laos by using time series data from 1985 to 2014. The data of FDI stock of Laos were collected from UNCTAD while GDP at constant price in 2005 was collected form World Bank. All time series data were tested stationary potential by Augment-Dickey Fuller test (ADF-test) and Phillip-Perron test (PP-test). In addition, the time series data were tested co-integration by using the Johansen co-integration approach to investigate long-run relationship. Short-run relationship and adjustment to equilibrium were examined by using Vector Error Correction Mechanism (VECM). stationary potential by using and PP-test
Contextual modulation of orientation tuning contributes to efficient processing of natural stimuli

It has been proposed that sensory neurons are adapted to the statistical structure of the natural environment in order to encode natural stimuli efficiently. While spatiotemporal correlations in luminance signals may be decorrelated by neurons in early visual processing stages, higher-order correlations, such as those in the orientation domain, are likely to persist in the input representation until the cortical level. In this study, we first examine orientation correlations in natural stimuli across brief time intervals and across nearby regions of space, and find strong correlations in both domains. We then examine contextual modulation of orientation tuning. We find that both temporal and spatial contexts exert a common influence on orientation tuning, shifting tuning away from the orientation of either the adapting (temporal) or surrounding (spatial) grating. Finally, we incorporate this context-mediated repulsive shift in orientation tuning into a model of cortical responses. We find that a direct result of the shift is a reduction of the redundancy in the population responses evoked by the orientation configurations that are most common in natural stimuli. Thus, cortical neurons may be adapted to the statistics of orientation in natural stimuli in order to increase the efficiency of natural stimulus representation.
Exploring new substance use settings

Substance use is a versatile activity, continuously spreading to new types of situations and contexts involving new substances and habits. In new and old user settings negotiations take place regarding the proper, risky, good, joyful, dangerous, or efficient way of acting. An important objective of substance use research is to keep track of and describe substance use and its logics, and so it must follow the prevalence of substances – new and old – in all user milieus, cultures, and contexts. In this issue of Nordic Studies on Alcohol and Drugs, readers will find new research on user contexts as well as the annually published Nordic alcohol statistics, this time for the period 2010–2015 (Hellman & Kettunen, 2017). Warne, Sinadinovic, Berman, Källmén, and Vinberg (2017) report results from their study on employees at ski resorts in northern Sweden. These resorts are a typical Nordic winter holiday milieu: millions of tourists visit resorts in Sweden, Norway, and Finland annually; Norway alone has more than 200 alpine ski resorts. In the most northern resorts, the winter sports season continues well into May. As in other alpine ski resorts in the world, the Nordic ones are filled with night life and other substance-use opportunities – as are the corresponding summer vacation resorts in southern Europe. While Nordic ski resorts are large seasonal night-time economies, there has not been much research on them as substance-use milieus. Previous research has shown that employees at tourist resorts tend to represent a high-risk population in terms of use of alcohol, drugs, and other negative lifestyle behaviours such as risky sexual conduct. Warne and colleagues (2017) proceeded with a questionnaire for ski resort employees, surveying different aspects of alcohol and drug use, psychosocial working conditions, and health. Compared to the general population, the ski resort employees scored higher on the AUDIT (Alcohol Use Disorders Identification Test) in all age groups except for men aged 35þ years. Furthermore, men in the 18–24 years age group scored higher on the corresponding test for drug use disorders identification. The prevalence of risky alcohol and drug use was higher among seasonally employed individuals than among those who were employed all year round. Certain variables seemed to
Experimental design and instability analysis of coaxial electrospray process for microencapsulation of drugs and imaging agents

Abstract. Recent developments in multimodal imaging and image-guided therapy requires multilayered microparticles that encapsulate several imaging and therapeutic agents in the same carrier. However, commonly used microencapsulation processes have multiple limitations such as low encapsulation efficiency and loss of bioactivity for the encapsulated biological cargos. To overcome these limitations, we have carried out both experimental and theoretical studies on coaxial electrospray of multilayered microparticles. On the experimental side, an improved coaxial electrospray setup has been developed. A customized coaxial needle assembly combined with two ring electrodes has been used to enhance the stability of the cone and widen the process parameter range of the stable cone-jet mode. With this assembly, we have obtained poly(lactide-co-glycolide) microparticles with fine morphology and uniform size distribution. On the theoretical side, an instability analysis of the coaxial electrified jet has been performed based on the experimental parameters. The effects of process parameters on the formation of different unstable modes have been studied. The reported experimental and theoretical research represents a significant step toward quantitative control and optimization of the coaxial electrospray process for microencapsulation of multiple drugs and imaging agents in multimodal imaging and image-guided therapy.
Trends in academic media: Open researcher and contributor identifier, concept and significance for the scientific research community

The contemporary scientific communication occurs in a digital environment and in professional virtual communities the concept of science is gradually transforming into the concept of e-science [1]. All participants of the scientific communication have already accepted the existence of Digital Object Identifier (DOI) number, as a digital content identifier of some object on the internet which is connected with e.g. a book or a journal article, regardless of the fact that their place on the internet may be changed [2]. The DOI is assigned to a scientific paper via the Crossref service, in order to find, cite, link and access scientific articles more easily. Likewise, steps have been taken to establish the identifier of an author’s unique identity. Back in 2006, Scopus presented its identification scheme Scopus Author IDENTIFIER (ID), and in 2008, Web of Science (WoS) created its own service called ResearcherID, as a system of unique identification of authors [3, 4]. In October 2012, the service Open Researcher and Contributor ID (ORCID) was presented. The concept of this service has been introduced back in 2009, with the aim to include all of the previous schemes and create a central registry of unique identifiers of all participants in research, education, science, innovation, i.e. a registry of authors/contributors [5]. ORCID is supposed to provide a long-term international digital identity of researchers [6].
A Framework for Web Service Discovery Based on Ontology Similarity

With the rapid growth of published Web services, matchmaking of relevant Web services becomes a significant challenge. In this paper, we present a novel framework based on genetic algorithm and domain-ontology for semantic Web Service discovery. We calculate the similarity between any two abstract models of web services, and use a genetic algorithm-based optimization procedure which relies on a given sample data to achieve the combination of the model parameters for best performance. The results show the high-values of precision and recall in our framework, especially when the ontological matching is involved.
Androgens and insulin resistance in type 1 diabetic men

OBJECTIVE In healthy men, both high and low serum testosterone concentrations are associated with insulin resistance, whereas low concentration of sex hormone binding globulin (SHBG) is related to reduced insulin sensitivity. The aim of our study was to examine the association of sex hormones, SHBG, dehydroeplandrosterone (DHEAS) and insulin‐like growth factor binding protein‐1 (IGFBP‐1) on Insulin sensitivity in type 1 diabetic patients.
Antigen receptor engagement delivers a stop signal to migrating T lymphocytes.

We investigated the role of the T cell antigen receptor (TcR) in control of T cell migration in an in vitro system. We used T cells from transgenic mice bearing a TcR for the lysozyme peptide 48-62 bound to I-A(k) (3A9). T cells from the 3A9 TcR transgenic mice crawled on purified intercellular adhesion molecule-1 substrates, but strikingly, stopped upon interaction with the physiological ligand, i.e., the mouse I-A(k) with covalently attached hen egg white lysozyme peptide residues 48-62 complex. TcR-triggered stopping was reversible by treatment with adhesion-strengthening phorbol esters. The microtubule organizing center of stopped cells was positioned adjacent to the site of stable cell anchorage. Direct conversion of lymphocyte function associated-1 to the high-affinity conformation with antibodies also stopped T cells in a similar manner to antigen. Thus, physiological TcR engagement triggers a stop signal through lymphocyte function associated-1. We propose that the stop signal is an early and essential event in T cell activation that also will play an important role in control of T cell migration.
Presence of DNA of Human Papillomavirus 16 but No Other Types in Tumor-Free Tonsillar Tissue

ABSTRACT According to PCR, the prevalences of human papillomavirus (HPV) DNA were 6.3% (13 of 206) in tonsillitis or hypertrophic tonsillar tissues and 0.6% (1 of 174) in exfoliated cells from normal tonsils. HPV-16 was the only type detected in tonsillar tissues, but it did not appear to lead to L1 antibody production.
Influence of albumin supplementation on tacrolimus and cyclosporine therapy early after liver transplantation

Liver transplant recipients administered gelatin (GEL) rather than human albumin solution (HAS) can become profoundly hypoalbuminemic in the early postoperative period and often have hepatic dysfunction at this time. The combined effect of these two abnormalities could be an increase in the unbound (active) concentration of low‐extraction highly albumin‐bound drugs, such as tacrolimus (TAC). This may increase the efficacy and/or toxicity of such drugs. We prospectively compared the clinical outcome of 69 de novo liver transplant recipients randomized primarily to TAC or cyclosporine (CYA) and secondarily to HAS or GEL therapy during the first 14 days after liver transplantation. Antipyrine clearance on the 7th postoperative day was used as a measure of liver metabolic function. Serum albumin levels were significantly lower in both GEL arms than HAS arms during the first 14 days (P < .001). Although antipyrine clearance was similar in all four trial arms, it was intermediate between that found in historic healthy controls and patients with cirrhosis (P < .0001). Serum creatinine concentrations were significantly greater in the TAC plus GEL arm than the other three arms (P < .001). The linearized treated acute rejection rate was significantly greater in the TAC plus HAS arm than the other three arms (relative risk, 2.02; 95% confidence interval, 1.07 to 3.78; P = .03). These data indicate that excess nephrotoxicity can occur with TAC in liver transplant recipients with impaired hepatic metabolism who are administered GEL. In addition, supplementary albumin may reduce the efficacy of TAC in liver transplant recipients at a time when the risk for rejection is greatest.