Miracle-dz/UniFAR-FTUs huggingface dataset:
DIROM: an experimental design interactive system for directed mutagenesis and nucleic acids engineering

A computer system DIROM for oligonucleotide-directed mutagenesis and artificial gene design has been designed for better experimental planning and control. DIROM permits searching for optimal oligonucleotides with respect to certain important parameters, namely sufficient energy of oligonucleotide-target hybridization, the secondary structure of oligonucleotide and target DNA, the presence of alternate binding sites in the target DNA and terminal G/C pairs. It can also be used to plan polymerase chain reaction experiments, for optimal primer selection, in sequencing, etc. DIROM enables one to search for both existing and potential restriction sites, to perform vector + target sequence construction. The system consists of a set of original algorithms that formalize the empirical knowledge of oligonucleotide action as primers.
Factors affecting the Haemophilia Joint Health Score in children with severe haemophilia

Joint damage from bleeding episodes leads to physical or functional limitations in people with haemophilia. Various factors may influence the frequency and severity of joint damage. This study examined whether age, prophylaxis, history of high‐titre inhibitors (HTI) and bleeding events influenced the Haemophilia Joint Health Score (HJHS) in children. Medical and physiotherapy notes of boys with severe haemophilia, aged 4–18 years, were reviewed to identify factors associated with increased HJHS. The HJHS of 83 boys (median age: 11) ranged from 0 to 25, with 44/83 (53%) having a score of zero. The median HJHS was 0 (mean 2.6). In the non‐HTI group, the HJHS for boys on late prophylaxis was 2.68 times higher than those who started early and the HJHS was on average 10% higher for every additional recent bleed. In this group the odds of having a zero score fell by 30% for every year increase in age. Boys with a history of HTI had higher HJHS scores than the non‐HTI group, and age, number of recent bleeds and tolerized status were positively associated with HJHS. The score rose on average by 28% for every year of age and by 76% for non‐tolerized boys. This study provides further evidence supporting early prophylaxis use and the importance of immune tolerance therapy. The HJHS is a useful tool for identifying and tracking changes in joint health with respect to therapy or disease progression. With improvements in haemophilia treatment, the disproportionate number of zero scores will continue to make interpretation of the HJHS challenging.
Description of a dinucleotide repeat polymorphism in the human elastin gene and its use to confirm assignment of the gene to chromosome 7

Informative polymorphisms have been very difficult to detect in the elastin gene, and this has hampered the analysis of heritable connective tissue disorders, notably the Marfan syndrome. We have recently detected a dinucleotide repeat polymorphism in intron 17 of the human elastin gene consisting of 8 alleles with sizes between 161 and 175 bp. Analysis of 540 chromosomes from unrelated Caucasian individuals revealed a bimodal frequency distribution typical of (dC‐dA)n (dG‐dT)n repeat polymorphisms, with allele frequencies ranging from 0.004 (161 bp) to 0.574 (163 bp). As the elastin gene was originally assigned to chromosome 2q31‐ter and because more recent data have suggested an assignment to 7q11.1–21.1, we have genotyped a sub‐set of the CEPH pedigrees and carried out pairwise linkage analysis with markers on chromosomes 7 and 2. Lod‐scores of between +3.70 and +13.69 were obtained with markers spanning 7p13‐q22.1, whilst negative lod‐scores were observed with the chromosome 2 markers. Analysis of type II human ovarian teratomas placed the elastin gene within 11 cM of the centromere on chromosome 7. Additionally, we detected the dinucleotide repeat in human‐rodent cell hybrids containing chromosome 7, but not those containing chromosome 2. These data confirm the assignment of elastin to chromosome 7 and provide a new, highly informative marker for the analysis of heritable disorders of connective tissue for which elastin is a candidate gene.
Four‐Level Anterior Cervical Discectomy and Fusion With Plate Fixation: Radiographic and Clinical Results

OBJECTIVEAnterior cervical discectomy and fusion with plating is a common procedure performed for cervical spondylosis by spine surgeons. However, data on procedures involving 4 disc spaces are lacking. We report the outcomes of patients who underwent 4-level anterior cervical discectomy and fusion with plating at a single institution. METHODSBetween 1997 and 2006, 34 patients (19 females, 15 males; mean age, 58 years; age range, 38–83 years) underwent 4-level anterior cervical discectomy and fusion with plating based on a surgical database search. Only patients undergoing surgery at 4 contiguous disc levels were included. Data were collected in a retrospective fashion. Patients' demographics, symptoms, neurologic findings, and radiographic findings at admission were recorded. Long-term clinical and radiographic outcomes at last follow-up were analyzed. RESULTSTwenty-nine patients (85%) underwent anterior cervical discectomy and fusion with plating at C3–C7. Sixteen patients presented with neurologic deficits, of which 14 (88%) improved. None worsened after surgery. Minor complications occurred in 26 patients, including transient dysphagia in 18 (53%) and hoarseness in 3 (9%). Radiographic outcomes were available in 27 patients (median follow-up, 15 months; range, 4–71 months). The overall fusion rate was 92.6%. Stable fibrous nonunions were present in 2 patients; the chance of nonunion was 1.9% per level and 7% per patient. Adjacent-level disease occurred in 2 patients. CONCLUSIONIn carefully selected patients, 4-level anterior cervical discectomy and fusion with plating can be associated with high rates of fusion. The technique is safe and effective for managing multilevel cervical spondylotic myelopathy and may obviate the need for circumferential procedures.
Analysis of the Humoral Immune Response toChlamydia pneumoniae by Immunoblotting and Immunoprecipitation

ABSTRACT Chlamydia pneumoniae is a widely spread agent of respiratory tract infections in humans. A reliable serodiagnosis of the disease is hampered by the poor knowledge about immunodominant antigens in C. pneumoniae infections. We applied a novel strategy to identify immunogenic proteins of C. pneumoniae TW183 combining metabolic radiolabeling of de novo-synthesized chlamydial antigens with immunoprecipitation. By this technique C. pneumoniae antigens of approximately 160, 97 to 99, 60 to 62, 40, 27, and 15 kDa were detected in the vast majority of sera from patients with a current C. pneumoniae infection. By immunoblotting purified elementary bodies of C. pneumoniae TW183 with the same sera, only the 60- to 62-kDa antigen could be detected consistently. Sequential immunoprecipitation performed at different stages of the chlamydial developmental cycle revealed that the 60- to 62-kDa antigen is strongly upregulated after 24 to 48 h of host cell infection and is presented as a major immunogen in both C. pneumoniae-infected patients and mice. We conclude that, due to its high sensitivity and concurrent preservation of conformational epitopes, metabolic radiolabeling of chlamydial antigens combined with immunoprecipitation may be a useful method to reveal important immunogens in respiratory C. pneumoniae infection which might have been missed by immunoblot analysis.
High temperature surface tension measurement

Atmospheric radio frequency inductively coupled plasma (RF-ICP) is used as the high temperature heat source in this containerless method to measure the surface tension and viscosity of high melting point materials. Dynamics of melting, droplet formation, and drop detachment of a rod exposed to RF plasma are recorded. Using a three-dimensional model in which flow field, heat transfer, and phase change are solved, the melting process of the rod will be simulated. Comparing simulations and experiments, surface tension, and viscosity of ceramics can be obtained. Some preliminary results from the experiments for copper and alumina are reported in the present study.
Radiation Dose Consideration in Kidney Stone CT Examinations: Integration of Iterative Reconstruction Algorithms With Routine Clinical Practice.

OBJECTIVE The objective of our study was to evaluate three commercially available iterative reconstruction (IR) algorithms-ASiR, iDOSE, and SAFIRE-and conventional filtered back projection (FBP) on image quality and radiation dose in kidney stone CT examinations. MATERIALS AND METHODS During the 6-month study period, 684 unenhanced kidney stone CT examinations of consecutive adults were performed on 17 CT scanners (GE Healthcare [vendor 1], n = 12 scanners; Philips Healthcare [vendor 2], n = 2; Siemens Health-care [vendor 3], n = 3); these examinations were retrieved using dose-monitoring software (eXposure). A total of 347 kidney stone CT examinations were reconstructed using FBP, and 337 examinations were processed using IR (ASiR, n = 248; iDOSE, n = 50; SAFIRE, n = 39). The standard-dose scanning parameters for FBP scanners included a tube potential of 120 kVp, a tube current of 75-450 mA for vendor 1 and a Quality Reference mAs of 160-180 for vendor 3, and a slice thickness of 2.5 or 5 mm. The dose-modified protocol for the IR scanners included a higher noise index (1.4 times higher than the standard-dose FBP protocol) for vendor 1, a lower reference tube current-exposure time product for vendor 2 (150 reference mAs), and a lower Quality Reference mAs for vendor 3 (120 Quality Reference mAs). Three radiologists independently reviewed 60 randomly sampled kidney stone CT examinations for image quality, noise, and artifacts. Objective noise and attenuation were also determined. Size-specific dose estimates (SSDEs) were compared using ANOVA. RESULTS Significantly higher subjective and objective measurements of image noise were found in FBP examinations compared with dose-modified IR examinations (p < 0.05). The radiation dose was substantially lower for the dose-modified IR examinations than the standard-dose FBP examinations (mean SSDE ± SD: 8.1 ± 3.8 vs 11.6 ± 3.6 mGy, respectively) (p < 0.0001), but the radiation dose was comparable among the three IR techniques (ASiR, 7.8 ± 3.1 mGy; iDOSE, 7.5 ± 1.9 mGy; SAFIRE, 7.6 ± 3.2 mGy) (p > 0.05). CONCLUSION The three IRs enable 20-33% radiation dose reduction in kidney stone CT examinations compared with the FBP technique without any image quality concerns. The radiation dose and image quality were comparable among these three IR algorithms.
Rapid, accurate calculation of the s-wave scattering length.

Transformation of the conventional radial Schrödinger equation defined on the interval r ∈ [0, ∞) into an equivalent form defined on the finite domain y(r) ∈ [a, b] allows the s-wave scattering length a(s) to be exactly expressed in terms of a logarithmic derivative of the transformed wave function φ(y) at the outer boundary point y = b, which corresponds to r = ∞. In particular, for an arbitrary interaction potential that dies off as fast as 1/r(n) for n ≥ 4, the modified wave function φ(y) obtained by using the two-parameter mapping function r(y; ̄r,β) = ̄r[1 + 1/β tan(πy/2)] has no singularities, and a(s) = ̄r[1 + 2/πβ 1/φ(1) dφ(1)/dy]. For a well bound potential with equilibrium distance r(e), the optimal mapping parameters are ̄r ≈ r(e) and β ≈ n/2 - 1. An outward integration procedure based on Johnson's log-derivative algorithm [J. Comp. Phys. 13, 445 (1973)] combined with a Richardson extrapolation procedure is shown to readily yield high precision a(s)-values both for model Lennard-Jones (2n, n) potentials and for realistic published potentials for the Xe-e(-), Cs(2)(aΣ(u)(+)(3)), and (3, 4)He(2)(XΣ(g)(+)(1)) systems. Use of this same transformed Schrödinger equation was previously shown [V. V. Meshkov et al., Phys. Rev. A 78, 052510 (2008)] to ensure the efficient calculation of all bound levels supported by a potential, including those lying extremely close to dissociation.
Meta-analysis of short-term outcomes after laparoscopy-assisted distal gastrectomy.

AIM To elucidate the current status of laparoscopy-assisted distal gastrectomy (LADG) with regard to its short-term outcomes by comparing it with conventional open distal gastrectomy (CODG). METHODS Original articles published from January 1991 to August 2006 were searched in the MEDLINE, EMBASE, and Cochrane Controlled Trials Register. Clinical appraisal and data extraction were conducted independently by 2 reviewers. A meta-analysis was performed using a random effects model. RESULTS Outcomes of 1611 procedures from 4 randomized controlled trials and 12 retrospective studies were analyzed. Compared to CODG, LADG was a longer procedure (weighted mean difference [WMD] 54.3; 95% confidence interval [CI] 38.8 to 69.8; P < 0.001), but was associated with a lower associated morbidity (odds ratio [OR] 0.54; 95% CI 0.37 to 0.77; P < 0.001); this was most significant for postoperative ileus (OR 0.27; 95% CI 0.09 to 0.84; P = 0.02). There was no significant difference between the two groups in anastomotic, pulmonary, and wound complications and mortality. Duration from surgery to first passage of flatus was faster (WMD -0.68; 95% CI -0.85 to -0.50; P < 0.001) and the frequency of additional analgesic requirement (WMD -1.36; 95% CI -2.44 to -0.28; P = 0.01), and duration of hospital stay (WMD -5.51; 95% CI -7.61 to -3.42; P < 0.001) were significantly lower after LADG. However, a significantly higher number of lymph nodes were dissected by CODG (WMD -4.35; 95% CI -5.73 to -2.98; P < 0.001). CONCLUSION LADG for early gastric cancer is associated with a lower morbidity, less pain, faster bowel function recovery, and shorter hospital stay.
A conceptual model to facilitate transitions from primary care to specialty substance use disorder care: a review of the literature

Aim This article presents a conceptual model to help facilitate the transition from primary care to specialty substance use disorder (SUD) care for appropriate patients. Background Substance misuse is a common health condition among patients presenting to primary care settings and may complicate the treatment of chronic health conditions such as diabetes and hypertension. It is therefore critical that primary care providers be prepared to identify and determine appropriate treatment options for patients presenting with substance misuse. Methods We conducted a narrative review that occurred in three stages: literature review of health care transition models, identification of conceptual domains common across care transition models, and identification of SUD-specific model elements. Findings The conceptual model presented describes patient, provider, and system-level facilitators and barriers to the transition process, and includes intervention strategies that can be utilized by primary care clinics to potentially improve the process of transitioning patients from primary care to SUD care. Recognizing that primary care clinics vary in available resources, we present three examples of care practices along an intensity continuum from low (counseling and referral) to moderate (telephone monitoring) to high (intensive case management) resource demands for adoption. We also provide a list of common outcomes clinics might consider when evaluating the impact of care transition practices in this patient population; these include process outcomes such as patients’ increased knowledge of available treatment resources, and health outcomes such as patients’ reduced substance use and better quality of life.
The application of sodium dodecyl sulphate‐polyacrylamide gel electrophoresis to the taxonomic identification of the total body protein band profiles of Diplostomum spp. metacercariae (Digenea), parasites of fish eyes

Sodium dodecyl sulphate‐polyacrylamide gel electrophoresis has been used to determine the metacercariae (Mc) total body protein band profiles of different Diplostomum spp. Four species of fish were investigated, roach (Rutilus rutilus) infected with D. spathaceum Mc, gywniad (Coregonus laveratus) infected with D. coregonus Mc, ruff (Gymnocephalus cernua) infected with a Diplostomum species related to D. gasterostei Mc, and perch (Perca fluviatilis) infected with D. gasterostei Mc. The four species of Diplostomum Mc were distinguished by three different bands of molecular weight, Mr 55 500, 53 500 and 52 000. A homology of polypeptide component distribution was evident for D. gasterostei Mc, from P. fluviatilis, and D. coregonus Mc, from C. laveratus, the latter showing reduced protein concentrations between bands Mr 32 000–40 000. Critical analysis of Mc polypeptide patterns showed no evidence of contamination with lens, retina or vitreous humour host eye protein. Gross morphological data for the parasites was also considered in relation to different band profiles obtained for the Diplostomum spp. Mc. Band profile analysis in conjunction with other taxonomic tests proved to be a useful tool in the identification of unknown species.
Regulation of endothelial cell gap formation and barrier dysfunction: Role of myosin light chain phosphorylation

Endothelial cell (EC) contraction results in intercellular gap formation and loss of the selective vascular barrier to circulating macromolecules. We tested the hypothesis that phosphorylation of regulatory myosin light chains (MLC) by Ca2+/calmodulin‐dependent myosin light chain kinase (MLCK) is critical to EC barrier dysfunction elicited by thrombin. Thrombin stimulated a rapid (<15 sec) increase in [Ca2+]i which preceded maximal MLC phosphorylation (60 sec) with a 6 to 8‐fold increase above constitutive levels of phosphorylated MLC. Dramatic cellular shape changes indicative of contraction and gap formation were observed at 5 min with maximal increases in albumin permeability occurring by 10 min. Neither the Ca2+ ionophore, A23187, nor phorbol myristate acetate (PMA), a direct activator of protein kinase C (PKC), alone or in combination, produced MLC phosphorylation. The combination was synergistic, however, in stimulating EC contraction/gap formation and barrier dysfunction (3 to 4‐fold increase). Down‐regulation or inhibition of PKC activity attenuated thrombin‐induced MLC phosphorylation (∼40% inhibition) and both thrombin‐ and PMA‐induced albumin clearance (∼50% inhibition). Agents which augmented [cAMP]i partially blocked thrombin‐induced MLC phosphorylation (∼50%) and completely inhibited both thrombin‐ and PMA‐induced EC permeability (100% inhibition). Furthermore, cAMP produced significant reduction in the basal levels of constitutive MLC phosphorylation. Finally, MLCK inhibition (with either ML‐7 or KT 5926) or Ca2+/calmodulin antagonism (with either trifluoperazine or W‐7) attenuated thrombin‐induced MLC phosphorylation and barrier dysfunction. These results suggest a model wherein EC contractile events, gap formation and barrier dysfunction occur via MLCK‐dependent and independent mechanisms and are significantly modulated by both PKC and cAMP‐dependent protein kinase A activities. © 1995 Wiley‐Liss, Inc.
Understanding the Heterogeneity of Human Mobility Patterns: User Characteristics and Modal Preferences

Characterizing individual mobility is critical to understand urban dynamics and to develop high-resolution mobility models. Previously, large-scale trajectory datasets have been used to characterize universal mobility patterns. However, due to the limitations of the underlying datasets, these studies could not investigate how mobility patterns differ over user characteristics among demographic groups. In this study, we analyzed a large-scale Automatic Fare Collection (AFC) dataset of the transit system of Seoul, South Korea and investigated how mobility patterns vary over user characteristics and modal preferences. We identified users’ commuting locations and estimated the statistical distributions required to characterize their spatio-temporal mobility patterns. Our findings show the heterogeneity of mobility patterns across demographic user groups. This result will significantly impact future mobility models based on trajectory datasets.
A new tool for the quantitative analysis of dendritic filopodial motility

Dendritic filopodia are tiny and highly motile protrusions formed along the dendrites of neurons. During the search for future presynaptic partners, their shape and size change dynamically, with a direct impact on the formation, stabilization and maintenance of synaptic connections both in vivo and in vitro. In order to reveal molecular players regulating synapse formation, quantitative analysis of dendritic filopodia motility is needed. Defining the length or the tips of these protrusions manually, however, is time consuming, limiting the extent of studies as well as their statistical power. Additionally, area detection based on defining a single intensity threshold can lead to significant errors throughout the image series, as these small structures often have low contrast in fluorescent images. To overcome these problems, the open access Dendritic Filopodia Motility Analyzer, a semi‐automated ImageJ/Fiji plugin was created. Our method calculates the displacement of the centre of mass (CoM) within a selected region based on the weighted intensity values of structure forming pixels, selected by upper and lower intensity thresholds. Using synthetic and real biological samples, we prove that the displacement of the weighted CoM reliably characterizes the motility of dendritic protrusions. Additionally, guidelines to define optimal parameters of live cell recordings from dendritic protrusions are provided. © 2014 International Society for Advancement of Cytometry
Don’t Trust the Scientists! Rejecting the Scientific Consensus “Conspiracy”

Scholars assessing the public understanding of science have long regarded informing Americans about scientific facts as key to raising Americans’ scientific literacy. But many Americans appear to be aware of the scientific consensus and nonetheless reject it. The individuals who are aware of the scientific consensus and reject its tenets tend to distrust scientists. They also focus their rejection on particular issues for which they may be otherwise motivated. This rejection may be driven by elites, who argue against the scientific consensus on issues like climate change by asserting either that the science is unsettled or by contending that the scientific consensus is itself a conspiratorial ploy. Individuals’ patterns of beliefs seem to imply that they view scientific evidence they dislike as the result of a conspiracy.
IS ONLINE CONSUMER PRICE SENSITIVE? A COMPREHENSIVE FRAMEWORK AND IMPLICATIONS FOR DEVELOPING E-PRICING STRATEGIES

The explosive growth of Internet retailing has increased competition among firms selling online. This competition is based on higher price dispersion and price discrimination, having important customer behaviour implications, which affect firms’ profitability. This phenomenon has trigger a stream of research on online price dispersion, however not consensual. In this paper we review the empirical and theoretical literature on price levels at electronic markets We develop a comprehensive framework to better understand the drivers of price dispersion and price discrimination at Internet, examining its impacts on consumer behaviour - price sensitivity, price orientation or convenience orientation – and we discuss e-pricing strategic implications to e-retailers. Finally this paper presents some conclusions, which underlies directions for future research.