Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring peptide energy landscapes: A test of force fields and implicit solvent models

A biased Monte Carlo‐minimization/annealing conformational search was used to characterize five descriptions of the energy landscape for each of three model systems: the 20‐residue “trp‐cage” miniprotein, the 20‐residue “BS1” peptide, and the 17‐residue “U(1‐17)T9D” peptide. The EEF1 and SASA energy landscapes were studied as well as those defined by using the GB/ACE implicit water model with one of three protein force fields: CHARMM19, CHARMM22, and CHARMM22/CMAP. The lowest‐energy structures of the trp‐cage and BS1 peptides found for the EEF1 landscape have main‐chain root‐mean‐square deviations (rmsds) from the respective NMR structures of less than 2 Å; for U(1‐17)T9D, the deviation is less than 3 Å using EEF1. The main‐chain rmsd of the minimum‐energy trp‐cage conformation obtained for the GB/ACE/CHARMM22/CMAP landscape is less than 1 Å. However, this energy function strongly favored helical structures for the two peptides shown by NMR to form beta‐sheet structures. Brief annealing of the system following main‐chain conformational changes was found to enhance the exploration of low‐energy states. The thousands of simulations reported here suggest that the prediction of protein structure might be improved by the simultaneous use of a CMAP‐like description of the main chain and an EEF1‐like description of the solvent. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Understanding voluntary program performance : Introducing the diffusion network perspective

Voluntary programs have rapidly become a means for the public, private, and third sectors to regulate and govern complex societal problems. Following the rapid and widespread emergence of these programs, scholars have been active in mapping, exploring, and interrogating their design and performance. Considerable advances have been made in describing program design and context conditions, and the actors involved in the voluntary program that relate to program performance. Less is known, however, about how these conditions affect program performance. Starting with one of the dominant theories on voluntary programs, the club theory perspective, this article seeks to understand how different program design conditions interact to affect the performance of 26 voluntary programs for low carbon building and city development in Australia, the Netherlands, and the United States. Applying qualitative comparative analysis, the study finds that the club theory perspective has limited explanatory power for this specific set of cases. Iterative rounds of analysis indicate that a diffusion network perspective is the best complementary perspective for explaining the performance of this set of programs. The article concludes that, in situations of a non-homogeneous market of voluntary program participants, a focus on the programs’ diffusion networks helps to explain their performance. This has implications for the design and implementation of such programs.
Eculizumab, Bortezomib and Kidney Paired Donation Facilitate Transplantation of a Highly Sensitized Patient Without Vascular Access

A 43‐year‐old patient with end‐stage renal disease, a hypercoagulable condition and 100% panel reactive antibody was transferred to our institution with loss of hemodialysis access and thrombosis of the superior and inferior vena cava, bilateral iliac and femoral veins. A transhepatic catheter was placed but became infected. Access through a stented subclavian into a dilated azygos vein was established. Desensitization with two cycles of bortezomib was undertaken after anti‐CD20 and IVIg were given. A flow‐positive, cytotoxic‐negative cross‐match live‐donor kidney at the end of an eight‐way multi‐institution domino chain became available, with a favorable genotype for this patient with impending total loss of a dialysis option. The patient received three pretransplant plasmapheresis treatments. Intraoperatively, the superior mesenteric vein was the only identifiable patent target for venous drainage. Eculizumab was administered postoperatively in the setting of antibody‐mediated rejection and an inability to perform additional plasmapheresis. Creatinine remains normal at 6 months posttransplant and flow cross‐match is negative. In this report, we describe the combined use of new agents (bortezomib and eculizumab) and modalities (nontraditional vascular access, splanchnic drainage of graft and domino paired donation) in a patient who would have died without transplantation.
Cellular interactions in the generation of cytolytic T lymphocyte responses Analysis of the helper T cell pathway

Murine splenic lymphocytes exhibit a requirement for helper T cells for the induction of a cytolytic T lymphocyte response to suboptimal doses of allogeneic cells, membranes from allogeneic cells, or purified H‐2 antigen in liposomes. The conditions where a requirement for help is apparent are the same conditions where a dependence on splenic adherent cells (SAC) has been demonstrated (Weinberger, O. et al., Proc. Natl. Acad. Sci. USA 1980. 77: 6091). Help can be provided in the form of primed, radioresistant, Ly‐1+ spleen or lymph node cells or helper factor (interleukin 2, IL‐2). A factor generated from phytohemagglutinin‐stimulated human lymphocytes, when added to culture in the presence of antigen, bypassed the requirement for Ia+ SAC and helper cells. IL‐2 reconstituted the response to H‐2Kk in liposomes in cultures depleted of SAC, strongly suggesting that the helper cell must see antigen re‐expressed by an antigen‐presenting cell, whereas the prekiller does not. IL‐2 could be generated by culturing Ly‐1+ murine spleen cells with H‐2Kk pulsed on SAC.
Silicon-Proven, Per-Cell Retention Time Distribution Model for Gain-Cell Based eDRAMs

Gain-cell embedded DRAM (GC-eDRAM) is an interesting alternative to SRAM for reasons such as high density, low bitcell leakage, logic compatibility, and suitability for 2-port memories. The major drawbacks of GC-eDRAMs are their limited data retention times (RTs) and the large spread of RT across an array, which degrade energy-efficiency due to refresh cycles. While the array refresh rate can be determined according to circuit simulation or post-manufacturing calibration, there is a lack of analytical and statistical RT models for GC-eDRAM that could unveil the limiters and circuit parameters that lead to the large observed RT spreads. In this work, we derive the first comprehensive analytical model for the statistical distribution of the per-cell retention time of 2T-bitcell GC-eDRAMs, which is found to follow a log-normal distribution. The accuracy of the proposed retention time model is verified by extensive Monte Carlo and worst case distance circuit simulations and silicon measurements of an 0.18 μ test chip. Furthermore, a sensitivity analysis unveils the circuit parameters that have the highest impact on the RT spread. Interestingly, the variability of the threshold voltage of the write access transistor has a much higher impact on the RT spread than the variability of any other circuit parameter, including the storage node capacitor. This holds true under process scaling, for nodes as advanced as 28 nm, as shown through simulation. The insights gained from the retention time model help circuit designers achieve better GC-eDRAMs with longer RTs and sharper RT distributions. In addition, the herein presented model can be used as a basis to study the reliability/energy trade-off for GC-eDRAM usage in fault-tolerant VLSI systems.
Adaptive RFID Impedance Matching Based on Phase Difference for Oil Well Applications

Severe impedance mismatch problems due to the various environmental issues in downhole can greatly degrade the reliability of the radio-frequency identification (RFID) control system. In this brief, a new adaptive RFID impedance-matching system for oil well applications is presented, in which the measured real-time phase difference is employed to track the impedance mismatch information, while a variable capacitor array combined with a frequency sweep is used to rematch the mismatched impedance. Experiments have been performed and the results show that the impedance can be rematched perfectly when affected by from the various environmental influences.
Study of leg weakness in two commercial broiler flocks

The major causes of leg weakness/lameness were investigated in two male commercial broiler flocks. The numbers of dead and lame birds culled from the flocks each day were recorded by the flock managers. Forty-four lame birds and 22 sound birds were examined postmortem during a period of six weeks and the proximal and distal end of each femur, tibiotarsus and tarsometatarsus were examined histologically. Attempts were made to isolate bacteria and viruses from the proximal end of each femur. Blood samples were examined for antibodies to chicken anaemia virus (CAV), infectious bursal disease virus (IBDV) and Mycoplasma species. Bacterial chondronecrosis with osteomyelitis was identified in the proximal end of the femur of eight of the 44 lame birds, and in the proximal end of the tibiotarsus of a further bird (20.4 per cent). Gram-positive bacteria were present in all the lesions. Staphylococcus aureus was recovered from 62.5 per cent of the lesions confirmed by histology. Bacterial chondronecrosis associated with S aureus has thus been identified as an important cause of leg weakness in these commercial broilers. Lesions suggestive of the condition were visible macroscopically in only 11.1 per cent of the cases subsequently diagnosed by histology and bone histology is therefore required before a diagnosis can be excluded. Angular limb deformities (13.6 per cent) and spondylolisthesis (11.4 per cent) were the most common macroscopic lesions identified as causes of lameness. The overall incidence of tibial dyschondroplasia was similar in both the lame and sound broilers, but severe lesions were found only in lame birds (4.5 per cent).
Power spectral components of heart rate variability in different types of cardiac remodelling in hypertensive patients.

BACKGROUND The aim of the study was to evaluate whether there are any significant differences in cardiac autonomic regulation in distinct types of hypertensive cardiac remodelling. MATERIAL AND METHODS We examined 86 patients with mild to moderate essential hypertension (EH). The parameters of left ventricle (LV) were measured by echocardiography: the diastolic mass normalized for body surface area (LVMI) and relative wall thickness (RWT). All patients were divided into three groups: normal LV geometry (23), concentric left ventricular hypertrophy (LVH) (29) and eccentric LVH (34). The control group included 30 age and sex-matched healthy volunteers. For calculation of heart rate variability (HRV) 512 RR intervals in supine rest and passive tilt were measured. Power spectral analysis with fast Furrier transform was used to obtain the total power, low frequency (LF) power (from 0.003 to 0.14 Hz), high frequency (HF) power (from 0.15 to 0.40 Hz) and sympathovagal index (SVI) as LF:HF ratio. RESULTS The parameters of HRV did not differ significantly among the groups studied. In the group with normal LV geometry there was observed a good response to tilt test resulting in an increase of SVI in three times (from 2.4 +/- 0.3 to 7.2 +/- 0.4), while in patients with both types of LVH there were no significant changes in SVI or even an inverse reaction to passive tilt. In the group with normal geometry patients with higher meanings of RWT had higher LF power (r = 0.52, p < 0.01), while in patients with LVH the increasement of LVMI and RWT was associated with reduction of HRV (rr = -0.43, -0.36, p < 0.05, respectively). CONCLUSIONS Heart rate variability is significantly reduced in essential hypertension and is also closely connected with cardiac structure and function. Patients with normal LV geometry are characterized by a preserved response to tilt test. LVH produce significant disturbances of autonomic regulation possibly due to lower sensitivity of cardiac adrenoreceptors independently of the LVH pattern.
Influence of Vegetation on the In Situ Bacterial Community and Polycyclic Aromatic Hydrocarbon (PAH) Degraders in Aged PAH-Contaminated or Thermal-Desorption-Treated Soil

ABSTRACT The polycyclic aromatic hydrocarbon (PAH) contamination, bacterial community, and PAH-degrading bacteria were monitored in aged PAH-contaminated soil (Neuves-Maisons [NM] soil; with a mean of 1,915 mg of 16 PAHs·kg−1 of soil dry weight) and in the same soil previously treated by thermal desorption (TD soil; with a mean of 106 mg of 16 PAHs·kg−1 of soil dry weight). This study was conducted in situ for 2 years using experimental plots of the two soils. NM soil was colonized by spontaneous vegetation (NM-SV), planted with Medicago sativa (NM-Ms), or left as bare soil (NM-BS), and the TD soil was planted with Medicago sativa (TD-Ms). The bacterial community density, structure, and diversity were estimated by real-time PCR quantification of the 16S rRNA gene copy number, temporal thermal gradient gel electrophoresis fingerprinting, and band sequencing, respectively. The density of the bacterial community increased the first year during stabilization of the system and stayed constant in the NM soil, while it continued to increase in the TD soil during the second year. The bacterial community structure diverged among all the plot types after 2 years on site. In the NM-BS plots, the bacterial community was represented mainly by Betaproteobacteria and Gammaproteobacteria. The presence of vegetation (NM-SV and NM-Ms) in the NM soil favored the development of a wider range of bacterial phyla (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi) that, for the most part, were not closely related to known bacterial representatives. Moreover, under the influence of the same plant, the bacterial community that developed in the TD-Ms was represented by different bacterial species (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinobacteria) than that in the NM-Ms. During the 2 years of monitoring, the PAH concentration did not evolve significantly. The abundance of gram-negative (GN) and gram-positive (GP) PAH-degrading bacteria was estimated by real-time PCR quantification of specific functional genes encoding the α subunit of PAH-ring hydroxylating dioxygenase (PAH-RHDα). The percentage of the PAH-RHDα GN bacterial genes relative to 16S rRNA gene density decreased with time in all the plots. The GP PAH-RHDα bacterial gene proportion decreased in the NM-BS plots but stayed constant or increased under vegetation influence (NM-SV, NM-Ms, and TD-Ms).
Interest rate autonomy in the presence of exchange rate stability: evidence from 13 selected Asia Pacific countries

ABSTRACT A notable feature of the empirical research on the interest rate autonomy is that very few studies seek to determine whether the use of interest rate policy to fine-tune the exchange rate misalignments has been undermined by sterilised foreign exchange intervention. To overcome this deficiency, this study uses the open-economy Taylor rule as a policy reaction function in a standard macroeconomic model to specify the measures of independent interest rate policy reacts to the exchange rate and examines the empirical validity based on a sample of 13 selected Asia Pacific countries. Using the generalised method of moments, the findings provide some policy implications; the interest rate instrument can serve as a coordinating function to fine-tune the exchange rate misalignments for improving the macroeconomic stability and serve as an external shock absorber to avoid or mitigate impact of instability in the foreign capital market.
Amplification and sequence analysis of DNA flanking integrated proviruses by a simple two-step polymerase chain reaction method

We describe a two-step polymerase chain reaction method that can be used for the amplification of cellular DNA sequences adjacent to an integrated retroviral provirus. The technique involves a partly degenerate, arbitrary primer that will hybridize in the provirus-flanking cellular DNA. By using this primer in combination with a biotinylated provirus-specific primer, a provirus-cellular DNA junction fragment can be isolated from the nonspecific amplification products by using streptavidin-coated magnetic beads. A second amplification employing a nested provirus-specific primer and a biotinylated nondegenerate primer derived from the partly degenerate primer followed by purification with streptavidin-coated beads enhances the specificity and the efficiency of recovery of a fragment(s) containing the unknown flanking sequences. In addition to being relevant in studies of viral integration sites, the method should be generally useful to analyze DNA sequences either upstream or downstream from a known sequence.
Enhancement of laplacian EEnG from humans by means of an EMD-based method

Non-invasive recordings of intestinal myoelectrical activity (Electroenterogram, EEnG) are affected by very-low-frequency (VLF) interferences, respiration, ECG and movement artifacts. In order to identify the intestinal pacemaker activity (slow wave), VLF interferences and respiration should be removed from abdominal surface recordings. In this paper a method based on empirical mode decomposition is proposed to identify and cancel such interferences and to enhance external recordings of human EEnG. The study was carried out on 10 recording sessions in which it was acquired 3 surface EEnG signals by means of active laplacian electrodes, together with respiratory and ECG signals. The application of the proposed method permits to increase the signal-to-interference ratio of EEnG signals from − 7.9±3.3 dB to 6.1±2.7 dB. In addition, the method helps to identify the intestinal pacemaker activity from surface EEnG recordings: the dominant frequency of processed signals is 8.6±1.7 cpm which fits the frequency of the intestinal slow wave in the jejunum, whereas the dominant frequency of original signals was 1.6±1.1 cpm which is associated to VLF interferences.
Optimizing Memory Access Performance Using Hardware Assisted Virtualization in Retargetable Dynamic Binary Translation

Dynamic Binary Translation is one of the most efficient strategies for the simulation of System-on-Chips, with recent studies showing that a large part of the simulation time is spent in realizing memory accesses. Indeed, the simulation of each load and store instructions requires a software emulation of the hardware Memory Management Unit (MMU). In this work, we propose to realize memory accesses in hardware, taking advantage of the hardware-assisted virtualization capabilities that are now available in modern processors. To do so, we have to setup and maintain shadow page tables, like any regular hypervisor would do, running the entire simulator on a virtual CPU. Now, each load and store instructions can be translated to just a couple of load and store instruction, executing at regular speed, therefore avoiding entirely the overhead of the software emulation of hardware MMU. The goal of this paper is to explain how it can be done. To demonstrate our idea, we have implemented our approach in the QEMU retargetable DBT engine, speeding up the simulation by as much as 40%.
Complications of cutaneous surgery in patients who are taking warfarin, aspirin, or nonsteroidal anti-inflammatory drugs.

BACKGROUND AND DESIGN No controlled studies exist with regard to the risks of continuing therapy with warfarin sodium or platelet inhibitors or the benefits of briefly discontinuing therapy with these agents in patients who are undergoing cutaneous surgical procedures. Our objective was to determine the frequency of complications of cutaneous surgery in patients who were receiving warfarin or platelet inhibitors and to evaluate whether preoperative discontinuation reduces complications. A retrospective, controlled study was performed of complications of excisional and Mohs micrographic surgery in 653 patients who were being treated with warfarin or platelet inhibitors or with their medications being briefly withheld. RESULTS Severe complications of cutaneous surgery in patients who are taking warfarin or platelet inhibitors are uncommon, occur in 1.6% of cases, and are not significantly increased compared with complications in control subjects. Furthermore, there was no statistically significant reduction in the rates of severe complications in patients who had their medications preoperatively held. CONCLUSION Cutaneous surgery in patients who receive warfarin or platelet inhibitors is associated with a low risk of severe complications, not significantly reduced by brief preoperative discontinuation.
Therapeutic bond judgments: Congruence and incongruence.

OBJECTIVE The present study had 2 aims: (a) to implement West and Kenny's (2011) Truth-and-Bias model to simultaneously assess the temporal congruence and directional discrepancy between clients' and therapists' ratings of the bond facet of the therapeutic alliance, as they cofluctuate from session to session; and (b) to examine whether symptom severity and a personality disorder (PD) diagnosis moderate congruence and/or discrepancy. METHOD Participants included 213 clients treated by 49 therapists. At pretreatment, clients were assessed for a PD diagnosis and completed symptom measures. Symptom severity was also assessed at the beginning of each session, using client self-reports. Both clients and therapists rated the therapeutic bond at the end of each session. RESULTS Therapists and clients exhibited substantial temporal congruence in their session-by-session bond ratings, but therapists' ratings tended to be lower than their clients' across sessions. Additionally, therapeutic dyads whose session-by-session ratings were more congruent also tended to have a larger directional discrepancy (clients' ratings being higher). Pretreatment symptom severity and PD diagnosis did not moderate either temporal congruence or discrepancy at the dyad level; however, during sessions when clients were more symptomatic, therapist and client ratings were both farther apart and tracked each other less closely. CONCLUSIONS Our findings are consistent with a "better safe than sorry" pattern, which suggests that therapists are motivated to take a vigilant approach that may lead both to underestimation and to attunement to fluctuations in the therapeutic bond.
Comparison between diurnal distribution of onset of infarction in patients with acute myocardial infarction and circadian variation of blood pressure in patients with coronary artery disease

We analyzed the diurnal distribution of the onset of infarction in 636 patients with acute myocardial infarction (MI) and compared it with the circadian variation of blood pressure in 57 patients with coronary artery disease (CAD). In addition, we studied the modification of the circadian blood pressure variation during treatment with antianginal medications in 20 patients with CAD. A marked diurnal periodicity (p < 0.05) was observed for the onset of MI, with peaks seen in the late morning, late evening, and very early morning. The blood pressure in the patients with CAD was elevated in the morning, reduced in the late evening, and was the lowest in the very early morning. The peaks of onset of infarction temporally corresponded to the characteristic feature of blood pressure profile observed in the patients with CAD, that is, the morning rise, the late evening decline, and the very early morning reduction. Antianginal medications significantly reduced the blood pressure, not only during the day (p < 0.02) but also at night (p < 0.05). These observations suggest that the decline in blood pressure, as well as the morning surge in blood pressure, may be closely related to the onset of MI. Therefore, when treating patients with CAD with antianginal medications which can potentially reduce blood pressure, the effects on the circadian variation of blood pressure should be considered.