Miracle-dz/UniFAR-FTUs huggingface dataset:
Fingerprints of bonding motifs in DNA duplexes of adenine and thymine revealed from circular dichroism: synchrotron radiation experiments and TDDFT calculations.

Synchrotron radiation circular dichroism (SRCD) spectra were recorded for a family of 12 DNA duplexes that all contain nine adenines (A) and nine thymines (T) in each strand but in different combinations. The total number of AT Watson-Crick (WC) base pairs is constant (18), but the number of cross-strand (CS) hydrogen bonds between A and T varies between 0 and 16, the maximum possible. Eleven of the duplexes have one or more A tracts, and one duplex has T tracts. The signals due to hybridization were found from subtraction of spectra of single strands from spectra of the duplexes. The residual spectrum of the T-tract duplex T(9)A(9):A(9)T(9) (5'-3':3'-5') significantly differs from that of the A-tract duplex A(9)T(9):T(9)A(9), but only below 210 nm, which suggests that the signal in this region depends on the superhelicity of the duplex. A principal component analysis of all residual spectra reveals that spectra of A-tract duplexes can be obtained to a good approximation as a linear combination of just two basis spectra. The first component is assigned to the spectrum of 18 WC and 8 CS pairs, whereas the second component is that of 8 CS pairs. This interpretation is supported by separate experiments on duplexes of varying lengths but with similar arrangements of the A and T's and by experiments on two other duplex families of 14 and 30 base pairs. The best correlation is obtained by the assumption that cross-strand interactions occur as long as there are two adenine neighbors in a strand. Our data indicate that a circular dichroism spectrum of a duplex containing only A and T can simply be inferred from the number of WC base pairs and the number of CS interactions, and we provide reference spectra for these two interactions. Finally, time dependent density functional theory calculations of the circular dichroism spectra for an isolated WC base pair and two different CS base pairs (between adenine N-6 amine and thymine O-4 or between adenine C-2-H and thymine O-2) were performed to provide some additional support for the interpretation of the experimental spectra. We find large differences between the two calculated CS spectra. However, there is a reasonable qualitative agreement between the calculated WC and the C-2-H.O-2 CS spectra and those deduced from the experimental data.
A case study of hospital closure and centralization of coronary revascularization procedures.

BACKGROUND Despite nation-wide efforts to reduce health care costs through hospital closures and centralization of services, little is known about the impact of such actions. We conducted this study to determine the effect of a hospital closure in Calgary and the resultant centralization of coronary revascularization procedures from 2 facilities to a single location. METHODS Administrative data were used to identify patients who underwent coronary artery bypass grafting (CABG), including those who had combined CABG and valve procedures, and patients who underwent percutaneous transluminal angioplasty (PTCA) in the Calgary Regional Health Authority from July 1994 to March 1998. This period represents the 21 months preceding and the 24 months following the March 1996 hospital closure. Measures, including mean number of discharges, length of hospital stay, burden of comorbidity and in-hospital death rates, were compared before and after the hospital closure for CABG and PTCA patients. Multivariate analyses were used to derive risk-adjustment models to control for sociodemographic variables and comorbidity. RESULTS The number of patients undergoing CABG was higher in the year following than in the year preceding the hospital closure (51.6 per 100,000 before v. 67.3 per 100,000 after the closure); the same was true for the number of patients undergoing PTCA (129.8 v. 143.6 per 100,000). The burden of comorbidity was significantly higher after than before the closure, both for CABG patients (comorbidity index 1.3 before v. 1.5 after closure, p < 0.001) and for PTCA patients (comorbidity index 1.0 before v. 1.1 after, p = 0.04). After adjustment for comorbidity, the mean length of hospital stay was significantly lower after than before the closure for CABG patients (by 1.3 days) and for PTCA patients (by 1.0 days). The adjusted rates of death were slightly lower after than before the closure in the CABG group. The adjusted rates of death or CABG in the PTCA group did not differ significantly between the 2 periods. INTERPRETATION Hospital closure and the centralization of coronary revascularization procedures in Calgary was associated with increased population rates of procedures being performed, on sicker patients, with shorter hospital stays, and, for CABG patients, a trend toward more favourable short-term outcomes. Our findings indicate that controversial changes to the structure of the health care system can occur without loss of efficiency and reduction in quality of care.
Shielding of a Small Charged Particle in Weakly Ionized Plasmas

In this paper, we present a concise overview of our recent results concerning the electric potential distribution around a small charged particle in weakly ionized plasmas. A number of different effects which influence plasma screening properties are considered. Some consequences of the results are discussed, mostly in the context of complex (dusty) plasmas.
OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB

In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA) toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM) standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.
An agent model to support social network-based palliative care

A social health care system, and palliative care in particular, can be viewed as a social network of interacting patients and care providers. Each patient in the network has a set of capabilities to perform his or her intended daily tasks. However, some patients may not have the required capabilities to carry out their desired tasks. Consequently, different groups of care providers offer the patients support by providing them with a variety of needed services. Assuming there is a cost and resource limitations for providing care within the system, where each care provider can support a limited number of patients, the problem is to find a set of suitable care providers to match the needs of the maximum number of patients. In this paper, we propose a novel agent-based model to address this problem by extending the agent's capabilities using the benefit of the social network. Our assumption is that each agent, or patient, can cover its disabilities and perform its desired tasks through collaboration with other agents, or care providers, in the network. The goal of this work is to improve the quality of services in the network at both individual and system levels. On one hand, an individual patient wants to maximize his/her goals, while at the system level we want to achieve quality care for as many patients as possible with minimum cost. The performance and functionality of this proposed model have been evaluated based on various synthetic networks. The results demonstrate a significant reduction in the operational costs and enhancement of the service quality.
The effects of progressive resistance training for children with cerebral palsy

Objectives: To investigate the effects of progressive resistance training of quadriceps and hamstrings muscles in children with cerebral palsy (CP). Design: Pilot study using a repeated measures design with measurements at baseline, immediately after six weeks training then at four-week follow-up. Setting: The project was undertaken within the physiotherapy department of two special schools in Glasgow. Subjects: A convenience sample of eight children aged between six and 12 years, with hypertonic CP. Intervention: The subjects participated three times per week in a six-week, progressive, free-weight, strengthening programme. Outcome measures: Maximum isometric muscle strength and resistance to passive stretch were measured with a hand-held myometer. The Gross Motor Function Measure and a 10-metre timed walking test, were used to assess function and gait parameters respectively. Results: Muscle strength increased, with the quadriceps to hamstrings strength ratio moving towards normal. These changes were retained at follow-up. Muscle tone decreased and continued to decrease to follow-up. The standing (D) and walking, running and jumping (E) goal areas of the Gross Motor Function Measure showed improvement that continued towards follow-up. Walking speed and step rate increased. Conclusions: A future large-scale randomized controlled study would be of value to substantiate these results as the small convenience sample and lack of control group limit this study. However, the finding that no adverse effect accompanied the positive outcomes in strength and function may encourage clinicians to consider resistance training alongside standard therapeutic interventions.
One hundred cases of recurrent abdominal pain in children: diagnostic procedures and criteria for a psychosomatic diagnosis

Aims: To highlight the diagnostic difficulties involved in elucidating the aetiology of recurrent abdominal pain and to evaluate the use of special premises and criteria for the diagnosis of psychosomatic pain. Methods: The study included 100 consecutive cases of recurrent abdominal pain in 6 to 15 y‐old children who were evaluated at a special paediatric clinic for recurrent abdominal pain and who were followed for at least one year. The investigation included a semi‐structured questionnaire, laboratory investigations based on clinical data and diagnoses based on defined criteria. Three premises and seven criteria, based on the assumption that chronic negative stress can cause recurrent pain, were used for the diagnosis of psychosomatic pain. Results: When the presented premises and criteria were employed for the diagnosis of psychosomatic pain, nearly half of the cases (48%) of recurrent abdominal pain could be explained. An organic or possibly organic diagnosis was found in 25% of the cases. Fourteen children had a possible psychosomatic diagnosis and in 9 cases no known diagnosis could be reached. Conclusion. The presented premises and criteria for the diagnosis of psychosomatic pain can be helpful when diagnosing recurrent abdominal pain, but further validation is needed. According to these criteria, a psychosomatic diagnosis was common in this series, accounting for nearly half of the cases. A medical diagnosis was evident in a quarter of the cases.
Water Supply Facility Damage and Water Resource Operation at Disaster Base Hospitals in Miyagi Prefecture in the Wake of the Great East Japan Earthquake

Abstract Introduction The aim of this study was to shed light on damage to water supply facilities and the state of water resource operation at disaster base hospitals in Miyagi Prefecture (Japan) in the wake of the Great East Japan Earthquake (2011), in order to identify issues concerning the operational continuity of hospitals in the event of a disaster. Methods In addition to interview and written questionnaire surveys to 14 disaster base hospitals in Miyagi Prefecture, a number of key elements relating to the damage done to water supply facilities and the operation of water resources were identified from the chronological record of events following the Great East Japan Earthquake. Results Nine of the 14 hospitals experienced cuts to their water supplies, with a median value of three days (range = one to 20 days) for service recovery time. The hospitals that could utilize well water during the time that water supply was interrupted were able to obtain water in quantities similar to their normal volumes. Hospitals that could not use well water during the period of interruption, and hospitals whose water supply facilities were damaged, experienced significant disruption to dialysis, sterilization equipment, meal services, sanitation, and outpatient care services, though the extent of disruption varied considerably among hospitals. None of the hospitals had determined the amount of water used for different purposes during normal service or formulated a plan for allocation of limited water in the event of a disaster. Conclusion The present survey showed that it is possible to minimize the disruption and reduction of hospital functions in the event of a disaster by proper maintenance of water supply facilities and by ensuring alternative water resources, such as well water. It is also clear that it is desirable to conclude water supply agreements and formulate strategic water allocation plans in preparation for the eventuality of a long-term interruption to water services. MatsumuraT, OsakiS, KudoD, FurukawaH, NakagawaA, AbeY, YamanouchiS, EgawaS, TominagaT, KushimotoS. Water supply facility damage and water resource operation at disaster base hospitals in Miyagi Prefecture in the wake of the Great East Japan Earthquake. Prehosp Disaster Med. 2015;30(2):1-5 .
Clonality among ampicillin-resistant Enterococcus faecium isolates in Sweden and relationship with ciprofloxacin resistance.

OBJECTIVE To investigate clonal relationships in a nationwide sample of human Enterococcus faecium isolates. METHODS Biochemical fingerprinting (PhP (PhenePlate) typing) was used to compare 180 fecal ampicillin-resistant E. faecium (ARE) isolates with 169 matched fecal ampicillin-susceptible E. faecium (ASE) isolates from patients in 23 hospitals, collected in 1998, and to study 39 fecal ARE isolates from non-hospitalized individuals collected in 1998, and five ARE and 29 ASE isolates from the early 1990s. Representative ARE and ASE isolates were subjected to pulsed-field gel electrophoresis (PFGE) analysis of genomic DNA and sequencing of the regions encoding the fluoroquinolone targets of the enzymes GyrA and ParC. RESULTS Both PhP and PFGE results showed a higher homogeneity among ARE than among ASE isolates (P < 0.001). One PhP type (FMSE1) comprised 73% of the hospital ARE isolates (53% of ARE isolates from non-hospitalized individuals, and four of five ARE isolates from the early 1990s), but only 1% of the ASE isolates. PFGE of the hospital E. faecium isolates revealed that 23 of the 25 ARE isolates and one of the 22 ASE isolates were of one dominating type. High-level resistance to ciprofloxacin (MIC > 16 mg/L) was present in 91% of ARE isolates, whereas only low-level resistance (MIC 4-16 mg/L; 35% of isolates) was found among ASE isolates. One mutation in parC (codon 80) and one of two mutations in gyrA (codons 83 or 87) were detected in all ARE isolates tested with high-level ciprofloxacin resistance, but were lacking in ARE and ASE isolates with low-level ciprofloxacin resistance. CONCLUSION Most ARE isolates in Sweden were clonally related. High-level ciprofloxacin resistance was found in ARE isolates of PhP type FMSE1 as well as in other PhP types, but never in ASE isolates.
How to successfully implement extended producer responsibility: considerations from an economic point of view

This paper investigates the concept of extended producer responsibility (EPR) from an economic point of view. Particular importance will be placed on the concept of ‘economic feasibility’ of an EPR policy, which should guide decision-making in this context. Moreover, the importance of the core EPR principle of ‘integrating signals throughout the product chain’ into the incentive structure will be demonstrated with experiences from Germany. These examples refer to sales packaging consumption, refillable drinks packages and waste electrical and electronic equipment collection. As a general conclusion, the interaction between economic principles and technological development needs to be observed carefully when designing incentive-compatible EPR policies.
Implantation of the Completely Ossified Cochlea: An Image-Guided Approach

Objectives To report a novel modification of the cochlear drill-out procedure that uses customized microstereotactic frames as drill guides. Patient(s) A 34-year-old man with an 18-year history of profound bilateral hearing loss and completely ossified cochleae that underwent a previous unsuccessful conventional cochlear drill-out procedure in the contralateral ear. Interventions Image-guided cochlear implantation using customized microstereotactic frames to drill linear basal and apical cochlear tunnels. Main Outcome Measures Transfacial recess cochlear drill-out procedure with full electrode insertion. Results Two linear paths were drilled using customized microstereotactic frames targeting the proximal and distal basal turn followed by a full split array insertion. Postoperative imaging confirmed 2 cochlear tunnels straddling the modiolus with adequate clearance of the facial nerve and internal carotid artery. The patient received auditory benefit with device use and did not experience any surgical complication. Conclusion Successful cochlear implantation in the setting of total scalar obliteration poses a significant challenge. Image guidance technology may assist in navigating the ossified cochlea facilitating safe and precise cochlear tunnel drilling.
Field and Laboratory Evaluations of Soybean Lines Against Soybean Aphid (Hemiptera: Aphididae)

ABSTRACT The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), is a major pest of soybean, Glycine max (L.). Merr. , that significantly reduces yield in northern production areas of North America. Insecticides are widely used to control soybean aphid outbreaks, but efforts are underway to develop host plant resistance as an effective alternative management strategy. Here, previously identified resistant lines were evaluated in laboratory tests against field-collected populations of soybean aphid and in field-plot tests over 2 yr in South Dakota. Six lines previously identified with resistance to soybean aphid—Jackson, Dowling, K1639, Cobb, Palmetto and Sennari—were resistant in this study, but relatively high aphid counts on Tie-feng 8 in field plots contrasted with its previously reported resistance. Bhart-PI 165989 showed resistance in one of two laboratory tests, but it had relatively large aphid infestations in both years of field tests. Intermediate levels of soybean aphid occurred in field plots on lines previously shown to have strong (Sugao Zairai, PI 230977, and D75-10169) or moderate resistance to soybean aphid (G93-9223, Bragg, Braxton, and Tracy-M). Sugao Zairai also failed to have a significant proportion of resistant plants in two laboratory tests against aphids field-collected in 2008, but it was resistant in laboratory tests with aphids collected in 2002, 2005, and 2006. Overall, results showed that lines with Rag (i.e., Jackson) or Rag1 gene (i.e., Dowling) had low aphid numbers, whereas lines with Rag2 (i.e., Sugao Zairai, Sennari) had mixed results. Collectively, responses of soybean aphid populations in laboratory and field tests in 2008 resembled a virulence pattern reported previously for biotype 3 soybean aphids, but virulence in soybean aphid populations was variable and dynamic over years of the study. These results, coupled with previous reports of biotypes virulent to Rag1, suggest that deployment of lines with a single aphid-resistance gene is limited for soybean aphid management, and that deployment strategies relying on multiple resistance genes may be needed to effectively use plant resistance against soybean aphid.
Bayesian Penalized Methods for High-Dimensional Data

ZAKARIA S KHONDKER: BAYESIAN PENALIZED METHODS FOR HIGH-DIMENSIONAL DATA (Under the direction of Dr. Joseph G. Ibrahim and Dr. Hongtu Zhu) Big data presents the overwhelming challenge of estimating a large number of parameters, which is much larger than the sample size. Even for a simple linear model, when the number of predictors is larger than or close to the sample size, such model may be unidentifiable and the least squares estimates of regression coefficients can be unstable. To deal with such issue, we systematically investigate three Bayesian regularization methods with applications in imaging genetics. First, we develop a Bayesian lasso estimator for the covariance matrix and propose a metropolis-based sampling scheme. This development is motivated by functional network exploration for the entire brain from magnetic resonance imaging (MRI) data. Second, we propose a Bayesian generalized low rank regression model (GLRR) for the mean parameter estimation and combine this with factor loading method of covariance estimation to capture the spatial correlation among the responses and jointly estimate the mean and covariance parameters. This development is motivated by performing genome-wide searches for associations between genetic variants and brain imaging phenotypes from data collected by Alzheimer’s Disease Neuroimaging Initiative (ADNI). Third, we extend GLRR to longitudinal setting and propose a Bayesian longitudinal low rank regression (L2R2) to account for spatiotemporal correlation among the responses as well as estimation of full-rank coefficient matrix for standard prognostic factors. This development is motivated by genome-wide searches for associations between genetic variants and brain imaging phenotypes observed over time with a primary focus on role of aging and the interaction of age with genotype in affecting brain volume.
Development to Blastocyst Is Impaired When Intracytoplasmic Sperm Injection Is Performed with Abnormal Sperm from Infertile Mice Harboring a Mutation in the Protein Phosphatase 1cγ Gene1

Abstract Idiopathic azoospermia, characterized by abnormal spermatogenesis, is commonly treated by performing intracytoplasmic sperm injection (ICSI) with sperm retrieved from testicular biopsies. However, no controlled experiments have been performed using an animal model to assess the efficacy or safety of the procedure. We have performed ICSI with testicular sperm obtained in a similar manner from testes of male mice homozygous for a null mutation in the protein phosphatase 1cγ gene (PP1cγ) or those of their wild-type littermates. PP1cγ mutant testicular sperm are less resistant to sonication than are wild-type sperm and display a range of morphological abnormalities, similar to those reported for testicular sperm from idiopathic azoospermic men. PP1cγ mutant sperm are unable to support development to the blastocyst stage, resulting in arrested development either before or just after compaction. A comparison of testicular and epididymal sperm from wild-type males revealed that the epididymal sperm caused embryos to fragment at an elevated rate. These results suggest that ICSI with any kind of testicular sperm carries an increased risk of embryo fragmentation and that abnormal testicular sperm has an added risk of embryo wastage at later preimplantation stages.