Phase-dependent interference mechanisms in a three-level Lambda system driven by a quantized laser field

The dynamics of an atomic few-level system can depend on the phase of driving fields coupled to the atom if certain conditions are satisfied. This is of particular interest to control interference effects, which can alter the system properties considerably. In this article, we discuss the mechanisms of such phase control and interference effects in an atomic three-level system in $\Lambda$ configuration, where the upper state spontaneously decays into the two lower states. The lower states are coupled by a driving field, which we treat as quantized. This allows for an interpretation on the single photon level for both the vacuum and the driving field. By analyzing the system behavior for a driving field initially in non-classical states with only few Fock number states populated, we find that even though the driving field is coupled to the lower states only, it induces a multiplet of upper states. Then interference occurs independently in three-level subsystems in $V$ configuration, each formed by two adjacent upper states and a single dressed lower state.Comment: 7 pages, 6 figure

Off-grid solar photovoltaic systems for rural electrification and emissions mitigation in India

Over one billion people lack access to electricity and many of them in rural areas far from existing infrastructure. Off-grid systems can provide an alternative to extending the grid network and using renewable energy, for example solar photovoltaics (PV) and battery storage, can mitigate greenhouse gas emissions from electricity that would otherwise come from fossil fuel sources. This paper presents a model capable of comparing several mature and emerging PV technologies for rural electrification with diesel generation and grid extension for locations in India in terms of both the levelised cost and lifecycle emissions intensity of electricity. The levelised cost of used electricity, ranging from $0.46–1.20/kWh, and greenhouse gas emissions are highly dependent on the PV technology chosen, with battery storage contributing significantly to both metrics. The conditions under which PV and storage becomes more favourable than grid extension are calculated and hybrid systems of PV, storage and diesel generation are evaluated. Analysis of expected price evolutions suggest that the most cost-effective hybrid systems will be dominated by PV generation around 2018

Effects of Ambulant Myofeedback Training and Ergonomic Counselling in Female Computer Workers with Work-Related Neck-Shoulder Complaints: A Randomized Controlled Trial

Objective: To investigate the effects of ambulant myofeedback training including ergonomic counselling (Mfb) and ergonomic counselling alone (EC), on work-related neck-shoulder pain and disability. Methods: Seventy-nine female computer workers reporting neck-shoulder complaints were randomly assigned to Mfb or EC and received four weeks of intervention. Pain intensity in neck, shoulders, and upper back, and pain disability, were measured at baseline, immediately after intervention, and at three and six months follow-up. Results: Pain intensity and disability had significantly decreased immediately after four weeks Mfb or EC, and the effects remained at follow up. No differences were observed between the Mfb and EC group for outcome and subjects in both intervention groups showed comparable chances for improvement in pain intensity and disability. Conclusions: Pain intensity and disability significantly reduced after both interventions and this effect remained at follow-up. No differences were observed between the two intervention groups

Atomic-accuracy prediction of protein loop structures through an RNA-inspired ansatz

Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. This article introduces a modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA) protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth RNA-puzzle competition. These results establish all-atom enumeration as a systematic approach to protein structure that can leverage high performance computing and physically realistic energy functions to more consistently achieve atomic resolution.Comment: Identity of four-loop blind test protein and parts of figures 5 have been omitted in this preprint to ensure confidentiality of the protein structure prior to its public releas

Risk factors for the development of severe typhoid fever in Vietnam

Background Typhoid fever is a systemic infection caused by the bacterium Salmonella enterica serovar Typhi. Age, sex, prolonged duration of illness, and infection with an antimicrobial resistant organism have been proposed risk factors for the development of severe disease or fatality in typhoid fever. Methods We analysed clinical data from 581 patients consecutively admitted with culture confirmed typhoid fever to two hospitals in Vietnam during two periods in 1993–1995 and 1997–1999. These periods spanned a change in the antimicrobial resistance phenotypes of the infecting organisms i.e. fully susceptible to standard antimicrobials, resistance to chloramphenicol, ampicillin and trimethoprim-sulphamethoxazole (multidrug resistant, MDR), and intermediate susceptibility to ciprofloxacin (nalidixic acid resistant). Age, sex, duration of illness prior to admission, hospital location and the presence of MDR or intermediate ciprofloxacin susceptibility in the infecting organism were examined by logistic regression analysis to identify factors independently associated with severe typhoid at the time of hospital admission. Results The prevalence of severe typhoid was 15.5% (90/581) and included: gastrointestinal bleeding (43; 7.4%); hepatitis (29; 5.0%); encephalopathy (16; 2.8%); myocarditis (12; 2.1%); intestinal perforation (6; 1.0%); haemodynamic shock (5; 0.9%), and death (3; 0.5%). Severe disease was more common with increasing age, in those with a longer duration of illness and in patients infected with an organism exhibiting intermediate susceptibility to ciprofloxacin. Notably an MDR phenotype was not associated with severe disease. Severe disease was independently associated with infection with an organism with an intermediate susceptibility to ciprofloxacin (AOR 1.90; 95% CI 1.18-3.07; p = 0.009) and male sex (AOR 1.61 (1.00-2.57; p = 0.035). Conclusions In this group of patients hospitalised with typhoid fever infection with an organism with intermediate susceptibility to ciprofloxacin was independently associated with disease severity. During this period many patients were being treated with fluoroquinolones prior to hospital admission. Ciprofloxacin and ofloxacin should be used with caution in patients infected with S. Typhi that have intermediate susceptibility to ciprofloxacin

The JCMT Plane Survey: early results from the l = 30 degree field

We present early results from the JCMT Plane Survey (JPS), which has surveyed the northern inner Galactic plane between longitudes l=7 and l=63 degrees in the 850-{\mu}m continuum with SCUBA-2, as part of the James Clerk Maxwell Telescope Legacy Survey programme. Data from the l=30 degree survey region, which contains the massive star-forming regions W43 and G29.96, are analysed after approximately 40% of the observations had been completed. The pixel-to-pixel noise is found to be 19 mJy/beam, after a smooth over the beam area, and the projected equivalent noise levels in the final survey are expected to be around 10 mJy/beam. An initial extraction of compact sources was performed using the FellWalker method resulting in the detection of 1029 sources above a 5-{\sigma} surface-brightness threshold. The completeness limits in these data are estimated to be around 0.2 Jy/beam (peak flux density) and 0.8 Jy (integrated flux density) and are therefore probably already dominated by source confusion in this relatively crowded section of the survey. The flux densities of extracted compact sources are consistent with those of matching detections in the shallower ATLASGAL survey. We analyse the virial and evolutionary state of the detected clumps in the W43 star-forming complex and find that they appear younger than the Galactic-plane average

Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface

Protein-protein interactions are critical determinants in biological systems. Engineered proteins binding to specific areas on protein surfaces could lead to therapeutics or diagnostics for treating diseases in humans. But designing epitope-specific protein-protein interactions with computational atomistic interaction free energy remains a difficult challenge. Here we show that, with the antibody-VEGF (vascular endothelial growth factor) interaction as a model system, the experimentally observed amino acid preferences in the antibody-antigen interface can be rationalized with 3-dimensional distributions of interacting atoms derived from the database of protein structures. Machine learning models established on the rationalization can be generalized to design amino acid preferences in antibody-antigen interfaces, for which the experimental validations are tractable with current high throughput synthetic antibody display technologies. Leave-one-out cross validation on the benchmark system yielded the accuracy, precision, recall (sensitivity) and specificity of the overall binary predictions to be 0.69, 0.45, 0.63, and 0.71 respectively, and the overall Matthews correlation coefficient of the 20 amino acid types in the 24 interface CDR positions was 0.312. The structure-based computational antibody design methodology was further tested with other antibodies binding to VEGF. The results indicate that the methodology could provide alternatives to the current antibody technologies based on animal immune systems in engineering therapeutic and diagnostic antibodies against predetermined antigen epitopes

The effects of shoulder load and pinch force on electromyographic activity and blood flow in the forearm during a pinch task

The object of the current study was to determine whether static contraction of proximal musculature has an effect on the blood flow more distally in the upper extremity. Static contractions of muscles in the neck shoulder region at three levels (relaxed, shoulders elevated and shoulders elevated loaded with 4.95 kg each) were combined with intermittent pinch forces at 0, 10 and 25% of the maximum voluntary contraction (MVC). Blood flow to the forearm was measured with Doppler ultrasound. Myoelectric activity of the forearm and neck-shoulder muscles was recorded to check for the workload levels. Across all levels of shoulder load, blood flow increased significantly with increasing pinch force (21% at 10% MVC and by 44% at 25% MVC). Blood flow was significantly affected by shoulder load, with the lowest blood flow at the highest shoulder load. Interactions of pinch force and shoulder load were not significant. The myoelectric activity of forearm muscles increased with increasing pinch force. The activation of the trapezius muscle decreased with increasing pinch force and increased with increasing shoulder load. The precise mechanisms accounting for the influence of shoulder load remains unclear. The results of this study indicate that shoulder load might influence blood flow to the forearm

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges