Miracle-dz/UniFAR-FTUs huggingface dataset:
Urinary biomarkers in the early detection of acute kidney injury after cardiac surgery.

BACKGROUND AND OBJECTIVES Serum creatinine (Scr) does not allow for early diagnosis of acute kidney injury (AKI). The diagnostic utility of urinary kidney injury molecule-1 (KIM-1), N-acetyl-beta-D-glucosaminidase (NAG), and neutrophil gelatinase associated lipocalin (NGAL) was evaluated for the early detection of postoperative AKI in a prospective study of 90 adults undergoing cardiac surgery. Designs, setting, participants, & measurements: Urinary KIM-1, NAG, and NGAL were measured at 5 time points for the first 24 h after operation and normalized to the urinary creatinine concentration after cardiac surgery. Receiver-operating characteristic curves were generated and the areas under the curve (AUCs) compared for performance of biomarkers in detection of postoperative AKI. RESULTS Thirty-six patients developed AKI, defined as an increase in Scr of > or =0.3 mg/dl within 72 h after surgery. The AUCs for KIM-1 to predict AKI immediately and 3 h after operation were 0.68 and 0.65; 0.61 and 0.63 for NAG; and 0.59 and 0.65 for NGAL, respectively. Combining the three biomarkers enhanced the sensitivity of early detection of postoperative AKI compared with individual biomarkers: the AUCs for the three biomarkers combined were 0.75 and 0.78. The performance of combining biomarkers was even better among 16 early postoperative AKI patients with AUCs of 0.80 and 0.84, respectively. CONCLUSIONS The results of this study support that a combination of urinary biomarkers may allow for early detection of postoperative AKI after cardiac surgery before a rise in Scr.
Autoinducer-2 Quorum Sensing Contributes to Regulation of Microcin PDI in Escherichia coli

The Escherichia coli quorum sensing (QS) signal molecule, autoinducer-2 (AI-2), reaches its maximum concentration during mid-to-late growth phase after which it quickly degrades during stationary phase. This pattern of AI-2 concentration coincides with the up- then down-regulation of a recently described microcin PDI (mccPDI) effector protein (McpM). To determine if there is a functional relationship between these systems, a prototypical mccPDI-expressing strain of E. coli 25 was used to generate ΔluxS, ΔlsrACDBFG (Δlsr), and ΔlsrR mutant strains that are deficient in AI-2 production, transportation, and AI-2 transport regulation, respectively. Trans-complementation, RT-qPCR, and western blot assays were used to detect changes of microcin expression and synthesis under co-culture and monoculture conditions. Compared to the wild-type strain, the AI-2-deficient strain (ΔluxS) and -uptake negative strain (Δlsr) were >1,000-fold less inhibitory to susceptible bacteria (P < 0.05). With in trans complementation of luxS, the AI-2 deficient mutant reduced the susceptible E. coli population by 4-log, which was within 1-log of the wild-type phenotype. RT-qPCR and western blot results for the AI-2 deficient E. coli 25 showed a 5-fold reduction in mcpM transcription with an average 2-h delay in McpM synthesis. Furthermore, overexpression of sRNA micC and micF (both involved in porin protein regulation) was correlated with mcpM regulation, consistent with a possible link between QS and mcpM regulation. This is the direct first evidence that microcin regulation can be linked to quorum sensing in a Gram-negative bacterium.
The Role of sentinel lymph-node biopsy in managing lip squamous cell carcinoma patients without clinical evidence of nodal metastasis.

AIM Squamous cell carcinoma (SCC) of the lip is a common oral malignancy. Lymph node metastasis occurs lately in the natural history of the disease but it is associated with poor outcome. Sentinel lymph node biopsy (SLNB) is an option that determines the potentially affected lymph nodes especially in clinically negative-node patients. The study aims to determine the feasibility of SLNB as a reliable staging tool in N0 stage lip SCC patients. METHODS Eighteen patients with N0 stage lip SCC were enrolled in the study. They were subjected to SLNB using the injection of the radiocolloid material and the Blue dye. The procedure was followed by bilateral supraomohyoid neck dissection in all patients. The pathological results of the harvested sentinel lymph nodes (SLNs) were compared with that of the dissection specimen in each patient. RESULTS The patent blue dye could localize the SLN in 15/18 patients whilst the radioisotope scanning could successfully identify it in 17/18 patents. On average, 1.8 SLNs were harvested from each patient. Two of seventeen patients with identified SLNs (11.8%) have positive nodal metastases. One of them has two SLNs and the other has only one. No false negativity was reported in the study as all the excised SLNs reflected correctly the status of the lymph node basin. CONCLUSION Sentinel lymphadenectomy is a safe and feasible procedure in managing neck of patients with node-negative lip SCC. It can accurately stage these patients. KEYWORDS sentinel lymph node, lip, cancer.
Poly(propylene fumarate) and poly(DL-lactic-co-glycolic acid) as scaffold materials for solid and foam-coated composite tissue-engineered constructs for cranial reconstruction.

This pilot study investigates the osseointegration of four types of critical-size (1.5-cm diameter) rabbit cranial defect (n = 35) bone graft scaffolds. The first is a solid poly(propylene fumarate)/beta-tricalcium phosphate(PPF/beta-TCP) disk; the three remaining constructs contain a PPF/beta-TCP core coated with a 1-mm resorptive porous foam layer of PPF or PLGA [poly(DL-lactic-co-glycolic acid)], and bone marrow. Animals were killed at 6, 12, and 20 weeks. There was no evidence of a foreign body inflammatory response at any time during the study. Histomorphometric analyses of new bone formation sorted lineal and areal measures of new bone into three cranial layers (i.e., external, middle, and internal). Statistical analyses revealed significantly more bone in the PLGA foam-coated constructs than in the PPF foam-coated constructs (p < 0.03). No implant fixation was used; there is no strength at time 0. Twenty percent of all explants were tested for incorporation strength with a one-point "push-in" test, and failure ranged from 8.3 to 34.7 lb. The results of this study support the use of PPF as a biocompatible material that provides both a structural and osteogenic substrate for the repair of cranial defects.
The Glaucoma-associated Olfactomedin Domain of Myocilin Is a Novel Calcium Binding Protein*

Background: Myocilin is an extracellular protein linked to glaucoma but is of unknown structure and function. Results: The myocilin olfactomedin domain contains a buried calcium ion ligated by Asp-380. Conclusion: The myocilin olfactomedin domain binds calcium with an unprecedented ligand arrangement. Significance: The presence of calcium within the OLF domain provides new clues into normal myocilin function, myocilin glaucoma pathogenesis, and biomedically important olfactomedin domains. Myocilin is a protein found in the trabecular meshwork extracellular matrix tissue of the eye that plays a role in regulating intraocular pressure. Both wild-type and certain myocilin variants containing mutations in the olfactomedin (OLF) domain are linked to the optic neuropathy glaucoma. Because calcium ions are important biological cofactors that play numerous roles in extracellular matrix proteins, we examined the calcium binding properties of the myocilin OLF domain (myoc-OLF). Our study reveals an unprecedented high affinity calcium binding site within myoc-OLF. The calcium ion remains bound to wild-type OLF at neutral and acidic pH. A glaucoma-causing OLF variant, myoc-OLF(D380A), is calcium-depleted. Key differences in secondary and tertiary structure between myoc-OLF(D380A) and wild-type myoc-OLF, as well as limited access to chelators, indicate that the calcium binding site is largely buried in the interior of the protein. Analysis of six conserved aspartate or glutamate residues and an additional 18 disease-causing variants revealed two other candidate residues that may be involved in calcium coordination. Our finding expands our knowledge of calcium binding in extracellular matrix proteins; provides new clues into domain structure, function, and pathogenesis for myocilin; and offers insights into highly conserved, biomedically relevant OLF domains.
Accuracy of allele frequency estimation using pooled RNA‐Seq

For nonmodel organisms, genome‐wide information that describes functionally relevant variation may be obtained by RNA‐Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA‐Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High‐quality genotypes for individual voles, determined for 23 682 SNPs, provided information on ‘true’ allele frequencies; allele frequencies estimated from the pool were then compared with these values. ‘True’ frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele‐specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA‐Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.
Multi-frequency test access mechanism design for modular SOC testing

This paper investigates the applicability of multi-frequency test access mechanism (TAM) design for reducing the system-on-a-chip (SOC) test application time. Based on the bandwidth matching concept the proposed algorithms explore a larger solution space, which, as shown by experimental data, can lead to improved test application time.
Upgrading Efficiency and Behavior: Electricity Savings from Residential Weatherization Programs

Residential weatherization programs have become a major component of U.S. energy policy. Through these programs, households receive heavily subsidized energy efficiency upgrades as well as informational and behavioral treatments designed to encourage conservation. While previous work demonstrates that weatherization programs provide sizable energy savings, all have measured the composite effect of efficiency upgrades and behavioral treatments. In this paper, we present the first estimates which disentangle the energy savings provided by each of the individual interventions. Our results reveal that the actual energy savings achieved by the efficiency upgrades are substantially smaller than ex-ante, engineering predictions. Moreover, we present evidence that the energy savings provided by the simple behavioral interventions can exceed the savings resulting from the much more costly efficiency upgrades.
Interactions with Search Systems

Information seeking is a fundamental human activity. In the modern world it is frequently conducted through interactions with search systems. The retrieval and comprehension of information returned by these systems is a key part of decision making and action in a broad range of settings. Advances in data availability, coupled with new interaction paradigms and mobile and cloud computing capabilities, have created a diverse set of new opportunities for information access and use. In this comprehensive book for professionals, researchers, and students involved in search system design and evaluation, search expert Ryen White discusses how search systems can capitalize on these new capabilities, and how next-generation search systems must support higher-order search activities such as task completion, learning, and decision making. He outlines the implications of these changes for the evolution of search evaluation, as well as related challenges that extend beyond search systems in areas such as privacy and societal benefit.
A Quantitative Analysis of the English Lexicon in Wiktionaries and WordNet

A quantitative analysis of the English lexicon was done in the paper. The three electronic dictionaries are under examination: the English Wiktionary, WordNet, and the Russian Wiktionary. It was calculated the quantity of English words and meanings (senses) in these dictionaries. The distribution of words for each part of speech, the quantity of monosemous and polysemous words and the distribution of words by number of meanings were calculated and compared across these dictionaries. The analysis shows that the average polysemy, the number and the distribution of word senses follow similar patterns in both expert and collaborative resources with relatively minor differences.
Mutation analysis of the spastin gene (SPG4) in patients in Germany with autosomal dominant hereditary spastic paraplegia

Hereditary spastic paraplegias (HSP) comprise a genetically and clinically heterogeneous group of neurodegenerative disorders characterized by progressive spasticity and hyperreflexia of the lower limbs. Autosomal dominant hereditary spastic paraplegia 4 linked to chromosome 2p (SPG4) is the most common form of autosomal dominant hereditary spastic paraplegia. It is caused by mutations in the SPG4 gene encoding spastin, a member of the AAA protein family of ATPases. In this study the spastin gene of HSP patients from 161 apparently unrelated families in Germany was analyzed. The authors identified mutations in 27 out of the 161 HSP families; 23 of these mutations have not been described before and only one mutation was found in two families. Among the detected mutations are 14 frameshift, four nonsense, and four missense mutations, one large deletion spanning several exons, as well as four mutations that affect splicing. Most of the novel mutations are located in the conserved AAA cassette‐encoding region of the spastin gene. The relative frequency of spastin gene mutations in an unselected group of German HSP patients is approximately 17%. Frameshift mutations account for the majority of SPG4 mutations in this population. The proportion of splice mutations is considerably lower than reported elsewhere. © 2002 Wiley‐Liss, Inc.
Inherited Unconjugated Hyperbilirubinemia : Crigler Najjar Syndrome

CriglerNajjar syndrome is an inherited disorder that manifests as persistent unconjugated hyperbilirubinemia. It occurs due to a defect in bilirubin conjugation due to complete or partial deficiency of uridine 5’-diphosphate glucuronosyltransferase enzyme. It comprises type 1 with complete deficiency and type 2 with partial deficiency of the enzyme. An early diagnosis in CriglerNajjar syndrome type2 enhances life expectancy. We present a 40-day old male child with CriglerNajjar syndrome type 2 with a heterozygous missense mutation in exon 1 of the UGT1A1 gene.
Outcomes following Semicircular Canal Plugging

Objectives To examine audiometric outcomes, symptom control rates, and complication rates following semicircular canal plugging for superior semicircular canal dehiscence syndrome. Study Design Retrospective chart review. Setting Private, neurotologic tertiary referral center. Subjects and Methods Patients undergoing semicircular canal plugging for superior semicircular canal dehiscence syndrome from January 1, 2007, to December 31, 2012. Pre- and postoperative audiometry, vestibular testing, operative findings, and clinical symptoms were assessed through chart review. Results A total of 24 ears underwent a canal plugging procedure during the study period for superior canal dehiscence syndrome. Pre- and postoperative air conduction pure-tone averages were 21.1 and 22.5 dB (P = .42, not significant [NS]). The average pre- and postoperative word recognition scores were 95.8% and 95.1% (P = .48, NS). Vestibular evoked myogenic potential data showed reduced thresholds in 7 patients with canal dehiscence. Complications were limited to a single, temporary facial weakness. Complete symptom improvement was noted in 35.7% of all patients, while at least partial symptom improvement was found in over 80% of patients. Conclusion Semicircular canal plugging procedures are associated with excellent hearing outcomes and may reduce preoperative symptoms in patients with superior semicircular canal dehiscence.
Vincristine neurotoxicity in Charcot‐Marie‐Tooth syndrome

The case of a patient with Charcot‐Marie‐Tooth syndrome and diffuse large‐cell lymphoma, in whom a severe generalized weakness developed after the intravenous administration of vincristine (2 mg) during combination chemotherapy, is reported. Spontaneous resolution of the severe weakness occurred when teniposide was substituted for vincristine in the chemotherapy regimen.
Purification of CD47‐streptavidin fusion protein from bacterial lysate using biotin–agarose affinity chromatography

CD47 is a widely expressed transmembrane glycoprotein that modulates the activity of a plethora of immune cells via its extracellular domain. Therefore, CD47 plays important roles in the regulation of immune responses and may serve as targets for the development of immunotherapeutic agents. To make sure CD47 functionality is intact under the process of protein conjugation, CD47‐streptavidin fusion protein was expressed and purified because it can easily bind to biotin‐tagged materials via the unique biotin–streptavidin affinity. In this study, gene sequences of CD47 extracellular domain (CD47ECD) and core streptavidin (coreSA) with a total 834 bp were inserted into pET20b plasmid to construct recombinant plasmid encoding CD47‐SA fusion gene. After bacteria transformation, the CD47‐SA fusion protein was expressed by isopropyl‐β‐d‐thiogalactopyranoside (IPTG) induction. The collected bacteria lysate was loaded on biotinylated agarose to proceed the purification of CD47‐SA fusion protein. Due to the unexpected high affinity between biotin and coreSA, standard washing and elution approaches (e.g., varying pH, using biotin, and applying guanidine hydrochloride) reported for biotin–streptavidin affinity chromatography were not able to separate the target fusion protein. Instead, using low concentration of the non‐ionic detergent Triton X‐100 followed with alkaline buffer could efficiently weaken the binding between biotin and coreSA, thereby eluting out CD47‐SA fusion protein from the biotin agarose column. The purified CD47‐SA fusion protein was further characterized by molecular biology methods and its antiphagocytic functionality was confirmed by the phagocytosis assay. © 2016 American Institute of Chemical Engineers Biotechnol. Prog. , 32:949–958, 2016
Economic Policy Uncertainty and Learning: Theory and Evidence on Mutual Funds

Using the mutual fund industry as a laboratory, we demonstrate theoretically and empirically that economic policy uncertainty affects investment decisions through an information rather than real options channel. Specifically, we find that fund flow-performance sensitivity decreases in uncertainty and does so more strongly for funds with shorter track records. The evidence supports the implication of our model that investor learning about manager ability weakens when uncertainty increases. Further, the effect of uncertainty on learning impacts managerial incentives. Consequently, managers are less likely to engage in active management during periods of greater uncertainty, an effect increasing in career concerns.
Patients-to-healthcare workers HIV transmission risk from sharp injuries, Southern Ethiopia

Background: Accidental needlestick injury rate among healthcare workers in Hawassa is extremely high. Epidemiological findings proved the infectious potential of this injury contaminated with a Human Immunodeficiency Virus (HIV)-infected patient's blood. Objective: This study aimed at estimating the risk of HIV transmission from patients to healthcare workers in Hawassa City, Ethiopia. Method: A probabilistic risk model was employed. Scenario-based assumptions were made for the values of parameters following a review of published reports between 2007 and 2010. Parameters: HIV prevalence, needlestick injury rate, exposure rate, sero-conversion rate, risk of HIV transmission and cumulative risk of HIV transmission. Finding: Generally, healthcare workers in Hawassa are considered to be at a relatively low (0.0035%) occupational risk of contracting HIV – less than 4 in 100,000 of healthcare workers in the town (1 in 28,751 workers a year). The 30 years' maximum cumulative risk estimate is approximately five healthcare workers per 1000 workers in the study area. Still, this small number should be considered a serious matter requiring post-exposure prophylaxis following exposure to unsafe medical practice leading to HIV infection.
Self‐modeling based diagnosis of network services over programmable networks

In this paper, we propose a multilayer self‐diagnosis framework for network services within the software‐defined networking and network functions virtualization environments. The framework encompasses 3 main contributions: (1) the definition of multilayered templates to identify the components to supervise across the physical, logical, virtual, and service layers. These templates are also finer‐granular, extendable, and machine‐readable; (2) a topology‐aware and a service‐aware self‐modeling module that takes as input the templates, instantiates them, and generates an on‐the‐fly diagnosis model, which includes the physical, logical, and the virtual dependencies of network services; (3) a topology‐aware and a service‐aware root cause analysis approach that takes into account the network services views and their underlying network resources observations within the aforementioned layers to automate the diagnosis of programmable networks. We also present extensive simulations to prove and evaluate the following aspects: a fully automated diagnosis model generation and a fine‐grained and reduced uncertainty diagnosis of the root cause for network services failures including those of their underlying resources. We include in this extended paper relevant state‐of‐the‐art on topology and service aware diagnosis approaches for different types of network technologies, a deeper insight of our approach and problem formalization, and additional results.