Miracle-dz/UniFAR-FTUs huggingface dataset:
Subdomain II of α-Isopropylmalate Synthase Is Essential for Activity

Background: Isopropylmalate synthases (IPMSs) with and without a regulatory domain were found. Results: IPMS subdomain II is essential for activities and likely involved in acetyl-CoA binding-mediated conformation transition. Conclusion: The N-terminal domain and the two subdomains comprise the complete and independently functional catalytic module of IPMS. Significance: The IPMS catalytic module was defined and characterized, which inferred a probable feedback inhibition mechanism. The committed step of leucine biosynthesis, converting acetyl-CoA and α-ketoisovalerate into α-isopropylmalate, is catalyzed by α-isopropylmalate synthase (IPMS), an allosteric enzyme subjected to feedback inhibition by the end product l-leucine. We characterized the short form IPMS from Leptospira biflexa (LbIPMS2), which exhibits a catalytic activity comparable with that of the long form IPMS (LbIPMS1) and has a similar N-terminal domain followed by subdomain I and subdomain II but lacks the whole C-terminal regulatory domain. We found that partial deletion of the regulatory domain of LbIPMS1 resulted in a loss of about 50% of the catalytic activity; however, when the regulatory domain was deleted up to Arg-385, producing a protein that is almost equivalent to the intact LbIPMS2, about 90% of the activity was maintained. Moreover, in LbIPMS2 or LbIPMS1, further deletion of several residues from the C terminus of subdomain II significantly impaired or completely abolished the catalytic activity, respectively. These results define a complete and independently functional catalytic module of IPMS consisting of both the N-terminal domain and the two subdomains. Structural comparison of LbIPMS2 and the Mycobacterium tuberculosis IPMS revealed two different conformations of subdomain II that likely represent two substrate-binding states related to cooperative catalysis. The biochemical and structural analyses together with the previously published hydrogen-deuterium exchange data led us to propose a conformation transition mechanism for feedback inhibition mediated by subdomains I and II that might associated with alteration of the binding affinity toward acetyl-CoA.
Parameters associated with active caries lesions assessed by two different visual scoring systems on occlusal surfaces of primary molars - a multilevel approach.

UNLABELLED The aim of this in vivo study was to evaluate the association between several parameters related to children and to their teeth, and the presence of active carious lesions assessed by two different visual indices on occlusal surfaces of primary molars. OBJECTIVE Occlusal surfaces of 757 primary molars in 139 children (3-12 years old) were classified as sound, or having inactive or active carious lesions using the Nyvad criteria (NY) and the International Caries Detection and Assessment System (ICDAS-II) and a supplemental lesion activity assessment system (ICDAS-LAA). Several parameters related to the tooth and to the child were recorded. Associations between these parameters and the presence of active carious lesions on occlusal surfaces were evaluated using logistic multilevel analysis. METHODS Second primary molar teeth and children with high caries experience were more frequently with active occlusal carious lesions compared to sound and inactive occlusal carious lesions classified by both visual scoring systems. Teeth with a mature dental plaque on the occlusal surface and younger children had more active caries than inactive occlusal carious lesions (excluding sound teeth in the analysis). A previous visit to a dentist was related to a lower frequency of active occlusal carious lesions classified by NY only, and upper primary molars presented with higher numbers of active occlusal carious lesions classified by ICDAS-LAA. RESULTS Presence of mature dental plaque and tooth type are tooth-related variables associated with active carious lesions on occlusal surfaces of primary teeth, as well as anterior caries experience and age are variables related to the child.
Blue-Enriched Lighting for Older People Living in Care Homes: Effect on Activity, Actigraphic Sleep, Mood and Alertness.

OBJECTIVE Environmental (little outdoor light; low indoor lighting) and age-related physiological factors (reduced light transmission through the ocular lens, reduced mobility) contribute to a light-deprived environment for older people living in care homes. METHODS This study investigates the effect of increasing indoor light levels with blue-enriched white lighting on objective (rest-activity rhythms, performance) and self-reported (mood, sleep, alertness) measures in older people. Eighty residents (69 female), aged 86 ± 8 yrs (mean ± SD), participated (MMSE 19 ± 6). Overhead fluorescent lighting was installed in communal rooms (n=20) of seven care homes. Four weeks of blue-enriched white lighting (17000 K ≅ 900 lux) were compared with four weeks of control white lighting (4000 K ≅ 200 lux), separated by three weeks wash-out. Participants completed validated mood and sleep questionnaires, psychomotor vigilance task (PVT) and wore activity and light monitors (AWL). Rest-activity rhythms were assessed by cosinor, non-parametric circadian rhythm (NPCRA) and actigraphic sleep analysis. Blue-enriched (17000 K) light increased wake time and activity during sleep decreasing actual sleep time, sleep percentage and sleep efficiency (p < 0.05) (actigraphic sleep). Compared to 4000 K lighting, blue-enriched 17000 K lighting significantly (p < 0.05) advanced the timing of participants' rest-activity rhythm (cosinor), increased daytime and night-time activity (NPCRA), reduced subjective anxiety (HADA) and sleep quality (PSQI). There was no difference between the two light conditions in daytime alertness and performance (PVT). CONCLUSION Blue-enriched lighting produced some positive (increased daytime activity, reduced anxiety) and negative (increased night-time activity, reduced sleep efficiency and quality) effects in older people.
Approaches to High-Dimensional Covariance and Precision Matrix Estimations

This chapter introduces several recent developments for estimating large covariance and precision matrices without assuming the covariance matrix to be sparse. It explains two methods for covariance estimation: namely covariance estimation via factor analysis, and precision Matrix Estimation and Graphical Models. The low rank plus sparse representation holds on the population covariance matrix. The chapter presents several applications of these methods, including graph estimation for gene expression data, and several financial applications. It then shows how estimating covariance matrices of high-dimensional asset excess returns play a central role in applications of portfolio allocations and in risk management. The chapter explains the factor pricing model, which is one of the most fundamental results in finance. It elucidates estimating risks of large portfolios and large panel test of factor pricing models. The chapter illustrates the recent developments of efficient estimations in panel data models.
Systems integration via software risk management

This paper addresses an evolutionary process currently taking place in software engineering: the shift from hardware to software, where the role of software engineering is increasing and is becoming more central in systems integration. This shift also markedly affects the sources of risk that are introduced throughout the life cycle of a system's development-its requirements, specifications, architecture, process, testing, and end product. Risk is commonly defined as a measure of the probability and severity of adverse effects. Software technical risk is defined as a measure of the probability and severity of adverse effects inherent in the development of software. Consequently, risk assessment and management, as a process, will more and more assume the role of an overall cross-functional system integration agent. Evaluating the changes that ought to take place in response to this shift in the overall pattern leads to two challenges. One is the need to reassess the role of a new breed of software systems engineers/systems integrators. The other is the need to develop new and appropriate metrics for measuring software technical risk. Effective systems integration necessitates that all functions, aspects, and components of the system must be accounted for along with an assessment of most risks associated with the system. Furthermore, for software-intensive systems, systems integration is not only the integration of components, but is also; an understanding of the functionality that emerges from the integration. Indeed, when two or more software components are integrated, they often deliver more than the sum of what each was intended to deliver; this integration adds synergy and enhances functionality. In particular, the thesis advanced in this paper is that the process of risk assessment and management is an imperative requirement for successful systems integration; this is especially true for software-intensive systems. In addition, this paper advances the premise that the process of risk assessment and management is also the sine qua non requirement for ensuring against unwarranted time delay in a project's completion schedule, cost overrun, and failure to meet performance criteria. To achieve the aspired goal of systems integration a hierarchical holographic modeling (HHM) framework, which builds on previous works of the authors, has been developed. This HHM framework constitutes seven major considerations, perspectives, venues, or decompositions, each of which identifies the sources of risk in systems integration from a different, albeit with some overlap, viewpoint: software development, temporal perspective, leadership, the environment, the acquisition process, quality, and technology.
Prostate Volume and Its Correlation with Histopathological Outcomes in Prostate Cancer

Introduction: There is a paucity of data investigating the relationship between histopathological variables of oncologic importance and prostate volume, and we aimed to investigate this. Patients and Methods: 2,207 consecutive patients who underwent robotic-assisted radical prostatectomy were studied. Preoperative demographic and both pre- and postoperative histopathological parameters were compared among the small (<40 cm3), intermediate (40–70 cm3), and large (>70 cm3) prostate groups. Results: Patients with smaller prostates were younger, had slightly lower BMIs, and lower prostate-specific antigen (PSA) levels than those with larger prostates (p < 0.001). They also had worse histopathological criteria (Gleason, core positivity, and maximum percent cancer) on preoperative biopsy and had worse radical specimen Gleason sums (p < 0.001), percent cancer (p < 0.001), and pathological stage (p = 0.016). 11.5% of the men in the small prostate group suffered a positive surgical margin (PSM) compared to 8.3 and 5.6% in the intermediate and large prostate groups, respectively (p = 0.008). Basilar, posterolateral, and multifocal PSMs were commoner in the small prostate group. Conclusions: Younger men have smaller prostates and worse preoperative histopathological parameters despite lower PSA values. Men with small prostates undergoing robotic-assisted radical prostatectomy have worse final Gleason sums, tumour volume, extraprostatic extension, and PSM rates than those with larger prostates.
Fine Needle Aspiration Cytology of Breast Lumps-A correlation with histopathology diagnosis

FNAC of breast lump is an important mode of diagnosis and forms a part of triple assessment. A retrospective study was undertaken at a tertiary hospital to know the feasibility and utility of fine needle aspiration of breast aspirates by comparing the diagnosis of malignancy with its histology. Of the 321 cases selected for the study, 93 cases were detected positive for malignancy. On reviewing, one case of false positivity and 5 cases of false negativity were detected. The sensitivity and specificity of FNAC for detecting malignancy was 98.27% and 99.49% respectively. Thus, we conclude that FNAC is a very important preliminary diagnostic test in palpable breast lumps and the results show a high degree of correlation with the final histopathology report.
Serum ß2-Microglobulin lin Patients with Monoclonal Gammopathies

Beta-2-microglobulin concentrations were determined in serum samples from 45 patients with benign and malignant monoclonal gammopathies. In the group of patients suffering from multiple myeloma or Waldenström macroglobulinemia the mean β2-microglobulin level was significantly higher than in the group with monoclonal gammopathy of undetermined significance. Values above 3 mg/L were highly indicative of a neoplastic process and were observed in all the Waldenström patients and in > 90% of myeloma patients. No significant correlation was noticed between β2-microglobulin and monoclonal protein levels in any of the groups examined.
Group B Streptococcal Prosthetic Knee Joint Infection Linked to the Consumption of Raw Fish

Introduction: Group B Streptococcal (GBS) prosthetic joint infections (PJI) are rare, accounting for only 4.6-6% of primary and revision total knee replacements (TKRs). In 2015, there was an outbreak of GBS infections in Singapore with an association confirmed between consumption of Chinese-style raw fish dishes (snakehead fish, Asian bighead carp) and GBS infection, Type III GBS ST283 strain, affecting more than 200 patients in Singapore. This outbreak is the largest of its kind in the world and also the first time that foodborne transmission of GBS has been proven. We present the first reported case in the literature of a confirmed PJI in a TKR related to foodborne transmission of GBS through consumption of raw fish (Snakehead fish). Case Report: Our patient is a 66-year-old Chinese female admitted with a 24-h history of acute right knee pain and swelling with associated fever in the context of consuming raw fish porridge 3 days before the onset of her symptoms. She had a TKR performed in the same knee 7 years before this presentation. Her GBS PJI was confirmed on both blood and intraoperative tissue/fluid cultures during the outbreak of GBS infections in Singapore. This was managed with debridement, polyethylene liner change, retention of metal prosthesis, and culture-directed antibiotics with good outcomes. Conclusion: Snakehead fish is a popular dish in the Asian community as a traditional remedy to promote wound healing after surgery. Our paper highlights the link between raw fish consumption and invasive GBS causing PJIs. This can occur in healthy adults, even in the absence of gastrointestinal symptoms, despite being a foodborne transmission. Our paper also highlights that GBS PJIs can be managed with debridement, antibiotic therapy, and implant retention with good outcomes in the setting of acute hematogenous infection. We recommend the inclusion of raw fish consumption on history taking in the workup of suspected PJIs and counseling patients preoperatively on the risk of GBS PJIs with the consumption of raw fish dishes (snakehead fish and Asian bighead carp) to mitigate unnecessary PJI risk.
Should cardiopulmonary resuscitation be performed on patients with heart failure? The role of the patient in the decision‐making process

Abstract. Ågård A, Hermerén G, Herlitz J (Lund University and Sahlgrens University Hospital, Göteborg, Sweden). Should cardiopulmonary resuscitation be performed on patients with heart failure? The role of the patient in the decision‐making process. J Intern Med 2000; 248: 279–286.
Unsupervised Similarity Learning from Textual Data

This paper presents a research on the construction of a new unsupervised model for learning a semantic similarity measure from text corpora. Two main components of the model are a semantic interpreter of texts and a similarity function whose properties are derived from data. The first one associates particular documents with concepts defined in a knowledge base corresponding to the topics covered by the corpus. It shifts the representation of a meaning of the texts from words that can be ambiguous to concepts with predefined semantics. With this new representation, the similarity function is derived from data using a modification of the dynamic rule-based similarity model, which is adjusted to the unsupervised case. The adjustment is based on a novel notion of an information bireduct having its origin in the theory of rough sets. This extension of classical information reducts is used in order to find diverse sets of reference documents described by diverse sets of reference concepts that determine different aspects of the similarity. The paper explains a general idea of the approach and also gives some implementation guidelines. Additionally, results of some preliminary experiments are presented in order to demonstrate usefulness of the proposed model.
Transduction of Aedes aegypti mosquitoes with vectors derived from Aedes densovirus.

Aedes densovirus (AeDNV)-based constructs that express green fluorescent protein (GFP) from either the P7 or the P61 promoter were made. The construct in which GFP protein was expressed as a fusion protein to the C-terminus of NS1 (NS1-GFP) showed the highest level of GFP expression. This hybrid NS1-GFP protein preserved the biological functions of the parental proteins: it showed GFP fluorescence, it stimulated expression from the virus promoters, and it facilitated rescue and replication of the cloned AeDNV genome. Similar to NS1, the hybrid NS1-GFP localized in the nucleus predominantly in a punctate pattern. Transducing virus particles carrying the NS1-GFP gene infected mosquito larvae. Expression of GFP was detected as early as 48 h postinfection and in larval and pupal stages. Midgut, hindgut, and Malpighian tubule cells expressed GFP soon after transduction. However, the anal papillae were the most commonly infected organ system. The anal papillae are syncytia and regulate ion concentration in the hemolymph of mosquito larvae, and they might be a novel route of mosquito larvae infection with densoviruses.
Secrecy Capacity of the Extended Wiretap Channel II with Noise

The secrecy capacity of an extended communication model of wiretap channelII is determined. In this channel model, the source message is encoded into a digital sequence of length N and transmitted to the legitimate receiver through a discrete memoryless channel (DMC). There exists an eavesdropper who is able to observe arbitrary μ = N α digital symbols from the transmitter through a second DMC, where 0 ≤ α ≤ 1 is a constant real number. A pair of an encoder and a decoder is designed to let the receiver be able to recover the source message with a vanishing decoding error probability and keep the eavesdropper ignorant of the message. This communication model includes a variety of wiretap channels as special cases. The coding scheme is based on that designed by Ozarow and Wyner for the classic wiretap channel II.
Harvey murine sarcoma virus p21 ras protein: biological and biochemical significance of the cysteine nearest the carboxy terminus.

Previous studies of premature chain termination mutants and in frame deletion mutants of the p21 ras transforming protein encoded by the transforming gene of Harvey murine sarcoma virus (Ha‐MuSV) have suggested that the C terminus is required for cellular transformation, lipid binding, and membrane localization. We have now further characterized the post‐translational processing of these mutants and have also studied two C‐terminal v‐rasH point mutants: one encodes serine in place of cysteine‐186, the other threonine for valine‐187. The Thr‐187 mutant was transformation‐competent, and its p21 protein was processed normally, as was the p21 encoded by a transformation‐competent deletion mutant from which amino acids 166‐175 had been deleted. The Ser‐186 mutant was defective for transformation. The p21s encoded by the Ser‐186 mutant and by the previously described transformation‐defective mutants did not undergo the posttranslational processing common to biologically active ras proteins: their electrophoretic migration rate did not change, they remained in the cytosol, and they failed to bind lipid. Since the cell‐encoded ras proteins also contain this cysteine, we conclude that this amino acid residue is required for all ras proteins.
The Effects of Managerial Values on Social Issues Evaluation: An Empirical Examination

This article suggests that due to the value-laden nature of social issues, managerial values, as a framework or schema, play an important role in the social issues evaluation process. Our data show that there is clearly a relationship between the issues managers evaluate as important and the values of those managers, with values being defined according to the Carroll typology—economic, legal, ethical, and philanthropic. It was apparent that the values held by the managers sampled determined how various sets of issues—community, political, and regulatory—were evaluated in terms of importance. This result suggests that the issues evaluation process, which should be objective, is not.
Innovation as a Learning Process: Embedding Design Thinking

There is a generic innovation process, grounded in models of how people learn, that can be applied across multiple sectors. It can be applied to the design and development of both hardware and software products, to the design of business models and services, to the design of organizations and how they work, and to the design of the buildings and spaces in which work takes place, or within which companies interact with their customers. This article describes such a model of innovation, grounding it in learning models and developing its implications for understanding, implementing, and engaging in the innovation process. The article focuses on the value and functions of multifaceted innovation teams. It notes the difficulties inherent in innovation efforts, shows where some of the pitfalls are for organizations attempting to innovate, and emphasizes the need to be flexible and adaptive in using the innovation process.
Multiple scansions in loanword phonology: evidence from Cantonese

In loanword phonology we seek to uncover the processes by which speakers possessing one phonological system perceive, apply native representational constraints on, and ultimately produce forms which have been generated by a different phonological system. We are interested in how speakers instantiate segmental and prosodic structure on an input which may or may not abide by native rules. Crucial to this assumed strategy is the idea that loanwords do not come equipped with their own phonological representation. For any phonetic string, it is only native speakers for whom a fully articulated phonological structure is present; as we will see, the input to loanword phonology is merely a superficial non-linguistic acoustic signal. Thus as host-language speakers perceive foreign forms in accordance with their indigenous phonological system, they instantiate native phonological representations on the acoustic signal, fitting the superficial input into the native phonological system as closely as possible.