Miracle-dz/UniFAR-FTUs huggingface dataset:
Matrigel: A complex protein mixture required for optimal growth of cell culture

Numerous cell types require a surface for attachment to grow and proliferate. Certain cells, particularly primary and stem cells, necessitate the use of specialized growth matrices along with specific culture media conditions to maintain the cells in an undifferentiated state. A gelatinous protein mixture derived from mouse tumor cells and commercialized as Matrigel is commonly used as a basement membrane matrix for stem cells because it retains the stem cells in an undifferentiated state. However, Matrigel is not a well‐defined matrix, and therefore can produce a source of variability in experimental results. In this study, we present an in‐depth proteomic analysis of Matrigel using a dynamic iterative exclusion method coupled with fractionation protocols that involve ammonium sulfate precipitation, size exclusion chromatography, and one‐dimensional SDS‐PAGE. The ability to identify the low mass and abundance components of Matrigel illustrates the utility of this method for the analysis of the extracellular matrix, as well as the complexity of the matrix itself.
The Detection of Bacteria on Microarrays Using Up-Converting Phosphor Nanoparticles as Fluorescent Labels

Nanoparticles containing the infrared-to-visible up-converting phosphors (UCP) ytterbium and erbium and co-doped with sodium yttrium fluoride were synthesized with diameters ranging from 30 nm to 50 nm. These high luminescence efficient UCP beads were employed as detection labels and applied in microarrays for the detection of specific nucleic acid hybrids to identify bacteria for the first time. The low cost of UCP nanoparticles and their detection equipment may facilitate their broad application in areas requiring large numbers of assays such as clinical diagnostic and environmental monitoring
Comparative X‐ray analysis of the un‐liganded fosfomycin‐target MurA

MurA, an essential enzyme for the synthesis of the bacterial cell wall, follows an induced‐fit mechanism. Upon substrate binding, the active site forms in the interdomain cleft, involving movements of the two domains of the protein and a reorientation of the loop Pro112‐Pro121. We compare two structures of un‐liganded MurA from Enterobacter cloacae: a new orthorhombic form, solved to 1.80 Å resolution, and a monoclinic form, redetermined to 1.55 Å resolution. In the monoclinic form, the loop Pro112‐Pro121 stretches into solvent, while in the new form it adopts a winded conformation, thereby reducing solvent accessibility of the critical residue Cys115. In the interdomain cleft a network of 27 common water molecules has been identified, which partially shields negative charges in the cleft and stabilizes the orientation of catalytically crucial residues. This could support substrate binding and ease domain movements. Near the hinge region an isoaspartyl residue has been recognized, which is the product of post‐translational modification of the genetically encoded Asn67‐Gly68. The homogenous population with L‐isoaspartate in both structures suggests that the modification in Enterobacter cloacae MurA is not a mere aging defect but rather the result of a specific in vivo process. Proteins 2000;40:290–298. © 2000 Wiley‐Liss, Inc.
MYCOBACTERIUM MANITOBENSE MASQUERADING AS CORYNEBACTERIUM PSEUDODIPHTHERITICUM IN A CASE OF POSTCATARACT SURGERY ENDOPHTHALMITIS.

PURPOSE To describe a case of postoperative Mycobacterium manitobense endophthalmitis with good visual outcome that is the first report of endophthalmitis by this organism. METHODS Clinical and microbiological description of a patient with postoperative endophthalmitis. RESULTS A 50-year-old chronic alcoholic man was referred to us with decreased vision in his right eye for 4 days. He had undergone cataract surgery with intraocular lens implantation in his right eye a month ago. The presenting vision in his right eye was counting fingers close to face. He was diagnosed as a case of postoperative endophthalmitis. Subsequently, the patient underwent pars plana vitrectomy and vitreous biopsy. The microbiologic investigation of the vitreous biopsy showed poorly stained gram-positive beaded bacilli that were acid fast, and growth in culture was identified as Corynebacterium pseudodiphtheriticum by Vitek 2 bacterial identification system. However, DNA analysis confirmed the organism to be M. manitobense. The patient responded well to repeat interventions with intravitreal antibiotics with a final reported visual acuity of 20/30 at 4 months after first intervention. CONCLUSION Although known to be an organism causing soft-tissue infections, M. manitobense can also cause postsurgical endophthalmitis. The diagnosis can be confused with Corynebacterium sp. on smear and culture. Subsequent DNA sequencing of the culture provides definite identification of the organism.
Intraoperative Neuromonitoring for Superior Semicircular Canal Dehiscence and Hearing Outcomes

Background Recent findings in patients with superior semicircular canal dehiscence (SCD) have shown an elevated ratio of summating potential (SP) to action potential (AP), as measured by electrocochleography (ECochG). Changes in this ratio can be seen during surgical intervention. The objective of this study was to evaluate the utility of intraoperative ECochG and auditory brainstem response (ABR) as predictive tools for postoperative hearing outcomes after surgical plugging via middle cranial fossa approach for SCD syndrome (SCDS). Methods This was a review of 34 cases (33 patients) in which reproducible intraoperative ECochG recordings were obtained during surgery. Diagnosis of SCDS was based on history, physical examination, vestibular function testing, and computed tomography imaging. Simultaneous intraoperative ECochG and ABR were performed. Pure-tone audiometry was performed preoperatively and at least 1 month postoperatively, and air-bone gap (ABG) was calculated. Changes in SP/AP ratio, SP amplitude, and ABR wave I latency were compared with changes in pure-tone average and ABG before and after surgery. Results Median SP/AP ratio of affected ears was 0.62 (interquartile range [IQR], 0.45–0.74) and decreased immediately after surgical plugging of the affected canal to 0.42 (IQR, 0.29–0.52; p < 0.01). Contralateral SP/AP ratio before plugging was 0.33 (IQR, 0.25–0.42) and remained unchanged at the conclusion of surgery (0.30; IQR, 0.25–0.35; p = 0.32). Intraoperative changes in ABR wave I latency and SP amplitude did not predict changes in pure-tone average or ABG after surgery (p > 0.05). Conclusion This study confirmed the presence of an elevated SP/AP ratio in ears with SCDS. The SP/AP ratio commonly decreases during plugging. However, an intraoperative decrease in SP/AP does not appear to be sensitive to either the beneficial decrease in ABGs or the mild high-frequency sensory loss that can occur in patients undergoing surgical plugging of the superior semicircular canal. Future work will determine the value of intraoperative ECochG in predicting changes in vestibular function.
A dual-mode dual-band bandpass filter using a single ring resonator

A dual-mode dual-band bandpass filter with two transmission poles in both of dual-passbands is presented with the proper stub-loading and external-excitation of a single microstrip ring resonator. By placing two excited ports at the 135°-separated positions along a uniform ring resonator, two 1storder degenerate modes, TM10 and TM01, can be simultaneously excited and they are split to produce two transmission poles in the 1st passband. Meanwhile, two 2nd-order degenerate modes, TM20 and TM02, are split by attaching four identical open-circuited stubs to the ring in a symmetrical manner with respect to two external ports. Thus, two transmission poles can be generated in both of dual passbands as demonstrated in theory. Finally, a compact dual-band ring resonator filter is designed and fabricated to operate at 2.3 and 4.8 GHz and its predicted results are verified in experiment.
Job Rationing in Recessions: Evidence from Work-Search Requirements

The last decade has seen a flurry of changes to unemployment insurance (UI) systems as policymakers have tried to shorten the unemployment rolls and support weak UI budgets. Many states have increased the work-search requirements for UI claimants in an effort to raise the disutility of claiming and match claimants with employers. However, the effects of these changes are initially unclear: canonical search-and-matching models suggest increased search effort will reduce unemployment, while job-rationing models suggest that the number of jobs is limited in weak labor markets. I compile novel data on work-search rules and use changes in them as plausibly exogenous variation in worker search effort. I show that increases in state UI search requirements are associated with increased search effort as measured by a number of proxies. However, these increased efforts translate into only marginally shorter unemployment durations on average. Using a number of different identification strategies, I show that there is heterogeneity in the effects across labor market conditions and that search requirements are relatively less effective in weak labor markets. The results suggest that the effectiveness of job-search policies may be limited by the rationing of jobs in recessions.
Identification and functionality of proteomes secreted by rat cardiac stem cells and neonatal cardiomyocytes

In the heart, the proteomes secreted by both cardiac stem cells (CSCs) and cardiac myocytes could act synergistically, but the identification and functionality of the proteins comprising the individual secretomes have not yet been described. In this study, we have identified proteins present in the media obtained from cultured rat CSCs and from cultured neonatal rat ventricular myocytes (NRVMs) and compared them with proteins identified in the media alone. Briefly, 83 unique proteins were identified after analysis by RPLC and MS. In total 49 and 23% were NRVM‐specific or CSC‐specific proteins, respectively, and 63% of total 83 proteins were integral plasma membrane and/or known secreted proteins. Fifteen proteins met our criteria for paracrine/autocrine factors: (i) robust protein identification, (ii) cell specific and (iii) known to be secreted. Most of these proteins have not been previously linked to stem cells. NRVM‐specific proteins atrial natriuretic factor (ANP) and connective tissue growth factor, and CSC‐specific protein interleukin‐1 receptor‐like 1 (ST2) were found to affect rat CSC proliferation. These findings suggest that relative concentration of each protein may be crucial for cellular intertalk and for the final outcome of cardiac cell therapy.
Prevalence of Painful Diabetic Peripheral Neuropathy among Patients with Diabetes Mellitus in the Middle East Region

The prevalence of painful diabetic peripheral neuropathy (DPN) was evaluated in type 1 or type 2 diabetes mellitus patients (n = 4097) attending outpatient clinics across the Middle East. Overall, 53.7% of 3989 patients with DN4 data met the criteria for painful DPN (Douleur Neuropathique-4 [DN4] scores ≥ 4). Significant predictors of painful DPN included long history (≥ 10 years) of diabetes (odds ratio [OR] 2.43), age ≥ 65 years (OR 2.13), age 50 – 64 years (OR 1.75), presence of type 1 versus type 2 diabetes (OR 1.59), body mass index ≥ 30 kg/m2 (OR 1.35) and female gender (OR 1.27). Living in one of the Gulf States was associated with the lowest odds of having painful DPN (OR 0.44). The odds of painful DPN were highest among patients with peripheral vascular disease (OR 4.98), diabetic retinopathy (OR 3.90) and diabetic nephropathy (OR 3.23). Because of the high prevalence and associated suffering, disability and economic burden of painful DPN, it is important that diabetic patients are periodically screened, using a simple instrument such as the DN4, and receive appropriate treatment if symptoms develop.
Popeye domain containing gene 2 (Popdc2) is a myocyte‐specific differentiation marker during chick heart development

The Popeye domain containing (popdc) genes constitute a novel gene family encoding proteins of the plasma membrane in muscle cells, with three N‐terminal transmembrane domains and a cytoplasmic carboxy terminus. In vertebrates, three members of the Popdc gene family have been described. However, in the chick system only two cDNAs, Popdc1 and Popdc3, have been cloned previously. By screening a chick expressed sequence tag database, we report here the identification of five alternatively spliced chick Popdc2 cDNAs with different carboxy termini. Northern blot analysis revealed expression of Popdc2 predominantly in the myocardium and weaker expression in skeletal muscle. By whole‐mount in situ hybridization, chick Popdc2 was first detected at Hamburger and Hamilton (HH) stage 7 within the anterior part of the heart fields. In the tubular heart, atrial and ventricular precursor cells stained positively for Popdc2. Weaker expression was observed in myocardium of the outflow tract and sinus venosus. By HH stage 18, the outer curvature myocardium was strongly stained, whereas expression in myocardium of the inner curvature was negligible. Popdc2 expression was absent from the endocardium and propepicardial organ. At HH stage 36, Popdc2 expression was confined to the compact layer myocardium. In addition to the heart, Popdc2 expression was also observed in the myotome and in the muscle‐forming fields of the limbs. Our results indicate that Popdc2 is highly expressed in the developing heart and may serve as a novel marker of myocardial differentiation in the chick embryo. Developmental Dynamics 229:695–702, 2004. © 2004 Wiley‐Liss, Inc.
Speech/pause detection algorithm based on the adaptive method of complementary decomposition and energy assessment of intrinsic mode functions

Speech/pause detection is one of the important tasks in processing. Its effectiveness depends on the accuracy of measuring amplitude, time, frequency and energy characteristics of speech signals. The main reason for large errors in measurements is due to the use of non-adaptive processing methods. The goal is to develop an algorithm for effective speech/pause detection on the basis of the adaptive method of complementary ensemble empirical mode decomposition (CEEMD). The algorithm is implemented using the adaptive processing method of CEEMD. The adaptability of methods lies in the fact that the basic functions used in the decomposition are extracted from the original speech signal, and allow us to take into account only its inherent features (hidden modulation, energy concentration regions, etc.). To carry out the research of the developed algorithm, a software package for mathematical modeling MATLAB was used. A speech/pause detection algorithm is developed on the basis of the adaptive method of complementary decomposition and energy estimation of empirical modes. A block diagram for the algorithm with a detailed mathematical description is presented. The advantages of the developed algorithm over the known analogs that have gained a wide practical popularity are indicated (STE + ZCR, IE and MFCC). The developed algorithm provides an increase in the correct detection rate of speech/pause by an average of 6%. Comparison of research results with analogs suggests that the developed algorithm is recommended for practical use in voice control systems (VCS).
Macrophage accumulation, division, maturation, and digestive and microbicidal capacities in tuberculous lesions. 3. The turnover of macrophages and its relation to their activation and antimicrobial immunity in primary BCG lesions and those of reinfection.

This work has changed our concept of the pathogenesis of tuberculosis. Formerly, tuberculous lesions were thought to be rather static, and macrophages were thought to become activated and develop antimicrobial immunity gradually. Now such lesions are thought to be dynamic. Macrophages constantly enter and constantly die, and the speed with which they become activated and increase their microbicidal ability seems to be of crucial importance.
Software Defect Prediction Using Dictionary Learning

—With the popularization of software version control system and defect tracking tools, large amounts of software development data is recorded. How to effectively use these data to improve the quality of software development, has become a hot topic in recent years. Software defect prediction technology can take full advantage of the historical data to build predictive models and automatically detect defective modules for efficient software test to improve the quality of a software system. But the class-imbalanced data makes the prediction model classifying a modules as a defective-free one easily, while the misclassification of defective modules generally incurs much higher cost risk than the misclassification of defective-free ones. To resolve this problem, we propose a cost-sensitive software defect prediction method using dictionary learning. It iteratively optimizes the classifier parameters and the dictionary atoms, to ensure that the extracted features (sparse representation) are optimal for the trained classifier; Moreover, we take the different misclassification costs into account, increasing the punishment on misclassification defective modules in the procedure of dictionary learning, making classification inclining to classify a module as a defective one. Experimental results on the 10 class-imbalanced data sets of NASA show that our method is more effective than other methods.
Antihypertensive medication use and incident Alzheimer disease: the Cache County Study.

BACKGROUND Recent reports suggest that antihypertensive (AH) medications may reduce the risk of dementing illnesses. OBJECTIVES To examine the relationship of AH medication use with incidence of Alzheimer disease (AD) among the elderly population (aged 65 years and older) of Cache County, Utah, and to examine whether the relationship varies with different classes of AH medications. METHODS After an initial (wave 1) multistage assessment (1995 through 1997) to identify prevalent cases of dementia, we used similar methods 3 years later (wave 2) to identify 104 incident cases of AD among the 3308 survivors. At the baseline assessment, we obtained a detailed drug inventory from the study participants. We carried out discrete time survival analyses to examine the association between the use of AH medications (including angiotensin converting enzyme inhibitors, beta-blockers, calcium channel blockers, and diuretics) at baseline with subsequent risk of AD. RESULTS Use of any AH medication at baseline was associated with lower incidence of AD (adjusted hazard ratio, 0.64; 95% confidence interval, 0.41-0.98). Examination of medication subclasses showed that use of diuretics (adjusted hazard ratio, 0.57; 95% confidence interval, 0.33-0.94), and specifically potassium-sparing diuretics (adjusted hazard ratio, 0.26; 95% confidence interval, 0.08-0.64), was associated with the greatest reduction in risk of AD. Corresponding analysis with a fully examined subsample controlling for blood pressure measurements did not substantially change our findings. CONCLUSIONS These data suggest that AH medications, and specifically potassium-sparing diuretics, are associated with reduced incidence of AD. Because the latter association is a new finding, it requires confirmation in further study.
Perceptions of HR practices, person–organisation fit, and affective commitment: The moderating role of career stage

In a three-wave survey study among 487 Dutch university employees, we examined how and when employees' perceptions of high-performance work practices (HPWP) affect employee affective commitment. We proposed that perceived person–organisation (PO) fit mediates this relationship and that the relationships among perceptions of HPWP, perceived PO fit, and affective commitment differ across career stages. Our results confirm that perceptions of HPWP enhance PO fit perceptions and, in turn, strengthen affective commitment. Moreover, the relationship between perceptions of HPWP and perceived PO fit is only significant among employees in the advancement stage of their careers; however, direct comparison across different career stages reveals no significant differences in the HPWP–PO fit relationship. Furthermore, career stage partly moderates the relationship between PO fit and affective commitment, which is only significant among employees in the maintenance career stage. These findings have important implications for the literature on strategic Human Resource Management and PO fit.
Neonatal periventricular-intraventricular hemorrhage: Subacute and chronic MR findings

Purpose: To evaluate MR findings at subacute and chronic stages after neonatal periventricular-intraventricular hemorrhage (PIVH), and to determine the clinical significance of follow-up MR. Material and Methods: Twenty-six children (estimated gestational age, 23-39 weeks; mean 29 weeks) with a history of previous PIVH underwent MR examination during their subacute and chronic clinical courses. PIVHs were initially detected with ultrasound examination in all cases. PIVH was divided into three grades (mild, moderate, and severe) according to the findings at the initial US studies, which were correlated to the MR findings. Results: Abnormal signal intensities related to hemorrhage were demonstrated in 10 of 21 patients (47.6%) on initial MR studies; the very low signal intensities on T2-weighted images found on the periventricular wall with a linear or a spotty shape had disappeared at one year after the initial US. The children with ventriculomegaly and periventricular leukomalacia (PVL) were increased in number on the follow-up studies. Conclusion: MR imaging provided valuable information about the consequences of neonatal PIVH such as developments of ventriculomegaly or PVL. It is noteworthy that hemorrhagic lesions could not be detected in half of the cases at the subacute or chronic stage of PIVH.
Measurement of the effects of cadmium stress on protozoan grazing of bacteria (bacterivory) in activated sludge by fluorescence microscopy

The effect of cadmium stress on protozoan bacterivory in sewage sludge was measured by experimentally exposing sludge communities to 0 to 150 mg of Cd per liter for up to 6 h and then determining the rates of protozoan grazing on bacteria, using a double-staining technique and epifluorescence microscopy. Bacterivory was measured by incubating the sludge with fluorescently labeled bacterium-sized latex beads and directly observing ingestion of the beads and bacterial cells in the sludge by epifluorescence microscopy of preserved samples. Staining with 4',6-diamidino-2-phenylindole and acridine orange permitted the simultaneous determination of protozoan numbers and bacterivory activity as estimated by the number of bacterial cells and bacterium-sized latex beads ingested by the representative ciliate Aspidisca costata. Enumeration with latex beads proved to be an effective way of estimating bacterivory in sludges subjected to heavy-metal stress. This technique should prove useful for determining the effects of other chemical stresses on protozoan numbers and bacterivory in organic-rich environments. Although the number of protozoa declined significantly only after exposure to 100 mg of Cd per liter for 4 h, grazing, as indicated by bead ingestion, was significantly inhibited by Cd concentrations of greater than 25 mg/liter in less than 1 h, and exposure to 100 mg of Cd per liter effectively stopped protozoan grazing within 1 h of exposure. Protozoan ingestion of latex beads and bacteria was inversely correlated to Cd concentration and exposure time. The reduction of protozoan bacterivory by Cd provides a possible explanation for the increase in suspended bacteria in the effluents of metal-stressed treatment facilities.