Miracle-dz/UniFAR-FTUs huggingface dataset:
Topographic study of arrestin using differential chemical modifications and hydrogen/deuterium exchange

Arrestin is involved in the quenching of phototransduction by binding to photoactivated and phosphorylated rhodopsin (P‐Rho*). To study its conformational changes and regions interacting with P‐Rho*, arrestin was subjected to (1) differential acetylation at lysine residues in the presence and absence of P‐Rho*, and (2) amide hydrogen/deuterium exchange. Labeled protein was proteolysed and analyzed by mass spectrometry. Three Lys residues, 28, 176, and 211, were protected from acetylation in native arrestin, although they were not located in regions exhibiting slow amide hydrogen exchange rates. The presence of P‐Rho* protected lysine 201 from acetylation and partially protected 14 other lysyl residues, including (2, 5), (163, 166, 167), (232, 235, 236, 238), (267, 276), (298, 300), and 367, where parentheses indicate lysine residues found within the same peptide. In contrast, in the C‐terminal region of arrestin, lysyl residues (386, 392, 395) were more exposed upon binding to P‐Rho*. These data allowed us to identify functional regions in the arrestin molecule.
Microbiological and clinical evaluation of the isolator lysis-centrifugation blood culture tube

In a controlled evaluation of 6,010 blood cultures, the yield of clinically significant microorganisms was greater from a lysis-centrifugation system (Isolator, Du Pont Co.) than from a nonvented vacuum bottle containing tryptic soy broth with sodium polyanetholesulfonate and CO2 and a vented bottle containing biphasic brain heart infusion medium with sodium polyanetholesulfonate. The Isolator significantly increased the frequency of isolation of Staphylococcus aureus and Candida spp. and significantly decreased the time required for the detection of S. aureus, Pseudomonas aeruginosa, and Candida spp. ; however, anaerobic bacteria were recovered significantly more frequently from nonvented bottles with tryptic soy broth, and pneumococci were recovered significantly more frequently from both bottle systems. Contamination of cultures was significantly greater with the Isolator system than with either bottle system. Regardless of the number of blood cultures obtained per septic episode, the Isolator detected microbiologically proven bacteremia or fungemia in a significantly greater number of patients and significantly decreased the time required for detection.
Integrating Thermal Physiology and Ecology of Ectotherms: A Discussion of Approaches

synopsis. An understanding of interactions between the thermal physiology and ecology of ectotherms remains elusive, partly because information on the relative performance of whole-animal physiological systems at ecologically relevant body temperatures is limited. After discussing physiological systems that have direct links to ecology (e.g., growth, locomotor ability), we review analytical methods of describing and comparing certain as? pects of performance (including optimal temperature range, thermal performance breadth), apply these techniques in an example on the thermal sensitivity of locomotion in frogs, and evaluate potential applications.
TOSI , DUQUESNOY , AND FERRARA

The serological analysis of h u m a n B cell a l loant igens has led to the def ini t ion of a HLAl i nked locus, des ignated H L A D R (1, 2), which codes for h u m a n Ia ant igens, i.e., h u m a n homologues o f m u r i n e Ia antigens. Thus far, 10 allospecificit ies have been assigned to this locus. Evidence has been accumula t ing over the past few years tha t h u m a n Ia ant igens are control led by at least two H L A l i n k e d loci. T h e first ind ica t ion was the discovery of a subset of Ia molecules car ry ing a n o n D R specificity DC1 by i m m u n o c h e m i c a l analysis at the molecular level (3). This d e t e r m i n a n t is cont ro l led by an allele at a separa te locus in s t rong l inkage d i sequ i l ib r ium wi th three alleles of the D R locus, DR1, DR2, and DRw6 (4, 5). S t ruc tu ra l charac te r iza t ion by microf ingerpr in t ing (6) and by two-dimensional electrophoresis (7) has shown tha t DC 1 molecules differ from D R molecules. This ident i f ica t ion of a second Ia locus has unvei led a basic homology of the h u m a n Ia system with the mur ine system in which two subsets of Ia molecules, I -A and I-E, exist (8). T h e e luc ida t ion of ano ther Ia specificity, BR4X7 (9) or H O N 7 (10), has revealed an add i t iona l complex i ty of the h u m a n Ia system. This specificity is cont ro l led also by an HLAl inked locus different from the D R locus and is t r ansmi t t ed in s t rong l inkage d isequi l ib r ium with the DR4, DR7, and D R w 9 alleles (5). BR4X7 could conceivably be allelic to DC 1 and thus be incorpora ted in a two-loci model . However , pep t ide m a p p i n g analysis showed that the molecules ca r ry ing B R 4 X 7 specificity are far more s imilar to D R molecules than to DC1 molecules, 1 lead ing to the assumpt ion tha t DC1 and BR4X7 m a y not be allelic. Consequent ly , a th i rd H L A l i n k e d Ia locus would be requi red to a c c o m m o d a t e BR4X7. Direct evidence for or against a three-loci hypothesis cannot be ob ta ined using the specificities DC1 and BR4X7 because they are always t r ansmi t t ed in repuls ion as a result of their associat ion with nonover l app ing sets of D R alleles. More comple te immunochemica l test ing of the three-loci concept requires the cons idera t ion of
Self-Assessments of Health by Korean Immigrant Women

The purpose of this study was twofold: to discover how Korean immigrant women perceived their health and to identify associations between social indicators and the health of Korean immigrant women. Participants in the study comprised a nonprobability sample of 137 Korean immigrant women living in the United States who submitted questionnaires about their health to the researcher by U.S. mail in 2004. Approximately 49% of the participants perceived their health as fair or poor. After age, income, education, marital status, and occupational status were controlled, the significant predictors of self-assessed health were involvement in exercise and length of residency in the United States. In future studies, the relationships between perception of health related to acculturation and self-rating health should be investigated.
The topical administration of bisphosphonates in implant surgery: a randomized split-mouth prospective study with a follow-up up to 5 years.

OBJECTIVE To evaluate the efficacy of the topical administration of bisphosphonates in implant therapy. MATERIALS AND METHODS Thirty-nine consecutive patients were selected for a split-mouth study. Inclusion criteria were: presence of a bilateral or total edentulism, ability to tolerate conventional implant procedures, older than 18 years. Ten patients were smokers. Ten patients were fully edentulous in both maxilla and mandible, 12 patients had fully edentulous maxilla or mandible, and 17 were bilaterally partially edentulous (9 in the mandible and 8 in the maxilla). A one-stage procedure was adopted in all cases. The prosthetic phase started 10 weeks after implant insertion. Each patient received implants on the control side and the test side, with insertion performed in the conventional way on the control side; on the test side, a 3% clodronate solution mixed with a surfactant (Tween-20) at a 1:3 ratio was topically administered both at the implant surface and at the implant site. RESULTS One hundred fifty-five implants were inserted. The test and control groups included 75 and 80 implants, respectively. The implant insertion torque was no less than 30 Ncm. A total of 7 implants failed in the control group (6 before loading and one after 12 months of loading). No failure occurred on the test side. By the 5-year follow-up, no further implant failure had been recorded. Overall, implant survival rates at 5 years for the test and control groups were, respectively, 100% and 91.3%, the difference being significant (p < .01). Mean marginal bone loss was 0.85 ± 0.71 mm in the test group and 1.12 ± 0.85 mm in the control group after 1 year of loading and stable thereafter. The difference was not significant. CONCLUSIONS The topical administration of bisphosphonates may positively affect implant survival in the preloading and postloading phases in partially and fully edentulous patients. However, a larger study population is needed to verify these promising clinical results.
Paclitaxel-Loaded Lipid Nanoparticles Prepared by Solvent Injection or Ultrasound Emulsification

ABSTRACT Lipid nanoparticles were fabricated as an injectable carrier system for paclitaxel. The components for the lipid matrix were based on phospholipids, and sucrose fatty acid ester was used as an emulsifier. Formulation prepared with solvent injection has a slightly larger particle size (187.6 nm) than the formulation (147.7 nm) prepared with ultrasound emulsification. Differential scanning calorimetry results indicated that paclitaxel entrapped in the lipid nanoparticles existed in an amorphous state in the lipid matrix. In vitro drug release was rather slow; only 12.5–16.5% of the drug released from the formulations within 14 days. Lipid nanoparticles demonstrated their potential as a promising pharmaceutical formulation of paclitaxel.
Identifying new bird species from differences in birdsong

The songs of birds, like human voices, are important elements of their identity. In ornithology, distinguishing the songs of different populations is as vital as identifying morphological and genetic differences. This paper takes a machine learning approach to the task. Using data gathered in Indonesia, the song from different subspecies of Black-naped Orioles and Olive-backed Sunbirds is examined. The song from different island populations is modelled with MFCCs and Gaussian Mixture Models. Analysing the performance of the classiﬁers on unseen test data can give an indication of song diversity. The results show that a forensic approach to birdsong analysis, inspired by speech processing, may offer invaluable insights into cryptic species diversity as well as song identiﬁcation at the subspecies level.
All digital wireless transceiver using modified BPSK and 2/3 sub-sampling technique

In this paper an all digital wireless transceiver is presented, with a proposed technique for data recovery. Communication is carried out on carrier frequency of 100 MHz with a local clock of 2/3 carrier frequency on the receiver side used to sub-sample incoming wireless signal and understand transmitted data. A modified BPSK is employed, which stretches periods of phase change to enable data recovery in our all digital circuit without clock recovery. The transceiver is implemented and tested on FPGA connected to coils to perform actual short range wireless communication. Our design uses no analog components and our target is to consume as low power as possible, which makes it suitable for low power applications like wireless image sensor nodes.
15-year prospective follow-up of patient-reported outcomes of late bowel toxicity after external beam radiotherapy for localized prostate cancer. A comparison with age-matched controls

We have previously described patient-reported outcomes of late side effects induced by conventional external beam radiotherapy (EBRT), 4 and 8 years after treatment, in 181 patients with localized prostate cancer compared with 141 age-matched controls. In the present study, we compare bowel side effects 15 years after EBRT with the same controls, and with the results of our previous 4-year and 8-year follow-ups. Of the 181 patients and 141 controls at the 4-year follow-up, 45 patients (25%) and 79 controls (56%) were still alive at the 15-year follow-up. Bowel symptoms were assessed using the symptom-specific questionnaire Prostate Cancer Symptom Scale (PCSS), which was sent to these 45 patients and 79 age-matched controls with a mean follow-up time of 15 years (162–197 months) after EBRT. The answer frequency was 64% in the patient group and 52% in the control group. The mean age was 78 years in both groups. At the 15-year follow-up, 39% of the patients and 84% of the controls reported no bowel problems (p <0.001), while 16% of the patients and 0% of the controls reported “Quite a few/many” problems with mucus in the stools (p <0.001). “Quite a bit/much” stool leakage was reported by 20% of the patients at the 15-year follow-up, in comparison to 4% of the patients at the 4-year follow-up (ns). The proportion of patients reporting late bowel symptoms was unchanged 15 years after EBRT in comparison to the 4-year follow-up. Increased bowel symptoms were seen in patients in comparison to the age-matched controls.
Growth and skeletal maturation after pediatric cardiac transplantation

Abstract: To examine the effects of cardiac transplantation on skeletal maturation and linear growth, we retrospectively evaluated annual bone age determinations and growth parameters of pediatric cardiac transplant recipients followed at our center. Included in the analysis were records of 86 patients (32 females) who had received a cardiac transplant at our institution between 1984 and 1998. Bone age delay of ≥12 months was apparent in 38.5% at the time of transplantation. At some point in their post‐transplant course, 23 patients (29%) had one or more bone age measurements that were ≥36 months delayed with respect to chronological age. Children transplanted before age seven and those with a pretransplantation diagnosis of cardiomyopathy experienced the most significant decrement in skeletal maturation after transplantation. High cyclosporin A levels and low body mass index were the only parameters found to be associated with delayed bone age. Although the majority of children grew at a normal rate after transplantation, height Z scores and height age were adversely affected regardless of the type of heart disease or the age at transplantation. The pathogenesis of both delayed skeletal maturation and growth retardation in this population warrant further investigation.
GP 2: efficient implementation of a graph programming language

The graph programming language GP (Graph Programs) 2 and its implementation is the subject of this thesis. The language allows programmers to write visual graph programs at a high level of abstraction, bringing the task of solving graph-based problems to an environment in which the user feels comfortable and secure. Implementing graph programs presents two main challenges. The first challenge is translating programs from a high-level source code representation to executable code, which involves bridging the gap from a non-deterministic program to deterministic machine code. The second challenge is overcoming the theoretically impractical complexity of applying graph transformation rules, the basic computation step of a graph program. The work presented in this thesis addresses both of these challenges. We tackle the first challenge by implementing a compiler that translates GP 2 graph programs directly to C code. Implementation strategies concerning the storage and access of internal data structures are empirically compared to determine the most efficient approach for executing practical graph programs. The second challenge is met by extending the double-pushout approach to graph transformation with root nodes to support fast execution of graph transformation rules by restricting the search to the local neighbourhood of the root nodes in the host graph. We add this theoretical construct to the GP 2 language in order to support rooted graph transformation rules, and we identify a class of rooted rules that are applicable in constant time on certain classes of graphs. Finally, we combine theory and practice by writing rooted graph programs to solve two common graph algorithms, and demonstrate that their execution times are capable of matching the execution times of tailored C solutions.
Major retinal cell components recognized by onchocerciasis sera are associated with the cell surface and nucleoli.

PURPOSE Cellular localization of the components recognized by onchocerciasis autoantibodies has not been investigated in any detail in cultured retinal cells. This study sought to examine, in cultured retinal cells, the subcellular localization of major components that cross-react with onchocerciasis sera. METHODS Immunofluorescence confocal laser scanning microscopy and Western blot analysis were carried out on adult pig retinal cells. RESULTS The onchocerciasis sera contain antibodies cross-reacting strongly with components of the surface and nucleoli in both the cultured retinal pigment epithelial and neural retinal cells. These epitopes are not recognized by the control sera obtained from noninfected individuals residing in an onchocerciasis hyperendemic area, and from those with or without ocular disease who have never been in any of the onchocerciasis hyperendemic countries. Double-labeling immunofluorescence microscopy does not detect any colocalization of a putative onchocerciasis autoantigen, calreticulin, and those cellular components recognized by onchocerciasis sera in either cell type. Furthermore, none of the onchocerciasis sera tested recognized recombinant calreticulin by Western blot analysis. CONCLUSIONS Major epitopes for onchocerciasis anti-retinal autoantibodies are associated with the surface and nucleolus components of retinal cells. Interaction of the onchocerciasis antibodies with the retinal cell surface molecules may play an important role in the development of ocular diseases initiated by the damage of retinal cells. Furthermore, the finding that the cellular components recognized by onchocerciasis sera do not colocalize with calreticulin, taken together with the observation of lack of recognition of recombinant calreticulin by these sera on Western blots, suggests that calreticulin is not a major onchocerciasis autoantigen.
The Structures of Domains of Blood Proteins

The regulatory proteinases of blood coagulation and fibrinolysis possess large non-catalytic regions linked to the N-terminal of a trypsin-like serine protease. The non-catalytic regions distinguish these enzymes from the more simple digestive ones which degrade proteins more or less indiscriminantly or simply process active peptides. The function of the non-catalytic segments is to oversee the binding of enzymes or proenzymes to other macromolecules or macro-structures, imparting recognition, which is the onset of a specificity that culminates in highly controlled regulation. The non-catalytic N-terminal regions of blood plasma proteases are generally organized into independent structural and functional domains consisting of four main types (1): a) kringle domains, b) vitamin K-dependent Ca-binding domains (Gladomains), c) growth factor domains and d) finger-type domains. All of these autonomous units are found repeatedly among the structures of blood proteins and fragments thereof. The kringle motif (Figure 1) is most abundant, occurring singly in urokinase, factor XII and vampire bat plasminogen activator, as pairs in prothrombin and tissue-type plasminogen activator (TPA), as a quadruplet in hepatocyte growth factor, a quintuplet in plasminogen and spectacularly, as 38 copies in the glycoprotein apolipoprotein (a). The occurrence of the other modules is almost equally impressive. The Gla-domain is a component of seven different proteins (prothrombin, factors VII, IX, X and the proteins designated C, S and Z) and the growth factor and finger domains also occur numerous times among these and other plasma proteins. The kringle domains consist of 80-85 residue, three disulfide, triple loop sequences (Figure 1) generally displaying about 50% conservation. The Gla-domain has about 48 residues, 70% conservation and is characterized by the presence of a conserved tetrapeptide disulfide loop and 9-12 Glu residues that were posttranslationally modified by a vitamin K-dependent carboxylase
Is it time to replace epileptic spikes with fast ripples?

In well over a century of performing epilepsy surgery, only 60%–65% of patients are, on average, seizure-free postoperatively.1 Despite multiple advances in neuroimaging and electrophysiologic techniques for localizing the epileptogenic zone and determining its boundaries, defining the exact amount of neuronal tissue required to resect in order to achieve postoperative seizure freedom remains challenging. The quest for a reliable biomarker of the epileptogenic zone continues. In addition to long-term intracranial EEG recordings to identify the seizure onset zone, cortical resections are also tailored in the operating room by including areas with abundant epileptic spikes and seizure-like interictal activity (ictiform patterns) recorded with corticography.2 Intraoperative localization based on interictal EEG activity would be much more cost-effective than chronic recording to capture spontaneous seizures.
Stimulation of Phosphorylation of Mitogen-Activated Protein Kinase by 1α,25-Dihydroxyvitamin D3 in Promyelocytic NB4 Leukemia Cells: A Structure-Function Study.

Recent studies have shown that 1α,25-dihydroxyvitamin D3[ 1α,25-(OH)2D3] actions in cell growth and differentiation are mediated by both its nuclear receptor (VDRnuc) and its rapid membrane-related effects. In the present study, we investigated the effect of 1α,25-(OH)2D3 on p42mapk phosphorylation using human acute promyelocytic leukemia cells (NB4). 1α,25-(OH)2D3 (10−8 m) significantly increased p42mapk phosphorylation in a time- and dose-dependent manner, with the earliest response detectable at 30 sec. Because 1α,25-(OH)2D3 is a conformationally flexible molecule, we have used a series of conformationally locked (6-s-cis vs. 6-s-trans) analogs to evaluate which shape is optimal for activation. Four 6-s-cis-locked analogs (HF, JM, JN, and JP) and two 6-s-trans-locked analog (JB and JD) were studied. HF, JM, JN, and JP all increased p42mapk phosphorylation at 1 and 5 min (10−8 m), but JB and JD had little effect. Analog HL [1β,25-(OH)2D3], a specific antagonist for only the rapid effects of 1α,25-(OH)2D.
Evidence for different pyoverdine-mediated iron uptake systems among Pseudomonas aeruginosa strains

Fourteen strains of Pseudomonas aeruginosa (P. aeruginosa ATCC 15692, P. aeruginosa ATCC 27853, and 12 clinical isolates) were checked for the production of pyoverdine and for pyoverdine-mediated iron uptake. Under iron restriction, two isolates produced undetectable amounts of pyoverdine, but all the other strains produced a compound with physicochemical properties identical or close to those of the pyoverdine of P. aeruginosa ATCC 15692 (strain PAO1). The pyoverdines were purified and tested for their growth-promoting activity and for their ability to facilitate 59Fe uptake in homologous experiments involving each pyoverdine and its producing strain, as well as in heterologous systems involving all the other strains. The results of both types of experiments suggested the existence of three specificity groups. This was confirmed by analysis of the amino acid composition of the pyoverdines, which differed for each group. A partially purified polyclonal antiserum raised against a major 80-kilodalton (kDa) iron-regulated outer membrane protein (IROMP) of P. aeruginosa PAO1 recognized the 80-kDa IROMPs from P. aeruginosa PAO1 and the clinical isolates belonging to the same group, whereas the IROMPs from the strains belonging to the two other groups were not detected. A second antiserum raised against the P. aeruginosa ATCC 27853 80-kDa IROMP gave similar results by reacting specifically with the 80-kDa IROMP from the strains belonging to this group. Thus, together with the already known pyoverdine from P. aeruginosa PAO1, two new types of pyoverdines produced by strains belonging to this species were characterized.