Efficient parallel processing with optical interconnections

With the advances in VLSI technology, it is now possible to build chips which can each contain thousands of processors. The efficiency of such chips in executing parallel algorithms heavily depends on the interconnection topology of the processors. It is not possible to build a fully interconnected network of processors with constant fan-in/fan-out using electrical interconnections. Free space optics is a remedy to this limitation. Qualities exclusive to the optical medium are its ability to be directed for propagation in free space and the property that optical channels can cross in space without any interference. In this thesis, we present an electro-optical interconnected architecture named Optical Reconfigurable Mesh (ORM). It is based on an existing optical model of computation. There are two layers in the architecture. The processing layer is a reconfigurable mesh and the deflecting layer contains optical devices to deflect light beams. ORM provides three types of communication mechanisms. The first is for arbitrary planar connections among sets of locally connected processors using the reconfigurable mesh. The second is for arbitrary connections among N of the processors using the electrical buses on the processing layer and N2 fixed passive deflecting units on the deflection layer. The third is for arbitrary connections among any of the N2 processors using the N2 mechanically reconfigurable deflectors in the deflection layer. The third type of communication mechanisms is significantly slower than the other two. Therefore, it is desirable to avoid reconfiguring this type of communication during the execution of the algorithms. Instead, the optical reconfiguration can be done before the execution of each algorithm begins. Determining a right configuration that would be suitable for the entire configuration of a task execution is studied in this thesis. The basic data movements for each of the mechanisms are studied. Finally, to show the power of ORM, we use all three types of communication mechanisms in the first O(logN) time algorithm for finding the convex hulls of all figures in an N x N binary image presented in this thesis

Molecular Beam Epitaxy Growth of Superconducting LiFeAs Film on SrTiO3(001) Substrate

The stoichiometric "111" iron-based superconductor, LiFeAs, has attacted great research interest in recent years. For the first time, we have successfully grown LiFeAs thin film by molecular beam epitaxy (MBE) on SrTiO3(001) substrate, and studied the interfacial growth behavior by reflection high energy electron diffraction (RHEED) and low-temperature scanning tunneling microscope (LT-STM). The effects of substrate temperature and Li/Fe flux ratio were investigated. Uniform LiFeAs film as thin as 3 quintuple-layer (QL) is formed. Superconducting gap appears in LiFeAs films thicker than 4 QL at 4.7 K. When the film is thicker than 13 QL, the superconducting gap determined by the distance between coherence peaks is about 7 meV, close to the value of bulk material. The ex situ transport measurement of thick LiFeAs film shows a sharp superconducting transition around 16 K. The upper critical field, Hc2(0)=13.0 T, is estimated from the temperature dependent magnetoresistance. The precise thickness and quality control of LiFeAs film paves the road of growing similar ultrathin iron arsenide films.Comment: 7 pages, 6 figure

Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection

Rice bacterial blight (BB) is a devastating rice disease. The Xa21 gene confers a broad and persistent resistance against BB. We introduced Xa21 into Oryza sativa L ssp indica (rice 9311), through multi-generation backcrossing, and generated a nearly isogenic, blight-resistant 9311/Xa21 rice. Using next-generation sequencing, we profiled the transcriptomes of both varieties before and within four days after infection of bacterium Xanthomonas oryzae pv. oryzae. The identified differentially expressed (DE) genes and signaling pathways revealed insights into the functions of Xa21. Surprisingly, before infection 1,889 genes on 135 of the 316 signaling pathways were DE between the 9311/Xa21 and 9311 plants. These Xa21-mediated basal pathways included mainly those related to the basic material and energy metabolisms and many related to phytohormones such as cytokinin, suggesting that Xa21 triggered redistribution of energy, phytohormones and resources among essential cellular activities before invasion. Counter-intuitively, after infection, the DE genes between the two plants were only one third of that before the infection; other than a few stress-related pathways, the affected pathways after infection constituted a small subset of the Xa21-mediated basal pathways. These results suggested that Xa21 primed critically important genes and signaling pathways, enhancing its resistance against bacterial infection

Cecal CircRNAs Are Associated With the Response to Salmonella Enterica Serovar Enteritidis Inoculation in the Chicken

Circular RNAs (circRNAs) are a class of endogenous noncoding RNA, which is different from linear RNA. CircRNA is an RNA molecule with a closed loop structure formed by reverse splicing. CircRNAs have been studied in several organisms, however, the circRNAs associated with the response to Salmonella enterica serovar Enteritidis (SE) inoculation in chickens are still unclear. In the current study, Jining Bairi chickens were inoculated with SE. CircRNAs involved in the response to SE inoculation were identified through next-generation sequencing. Our results showed that there were 5,118 circRNAs identified in the control and treated groups. There were 62 circRNAs significantly differentially expressed following SE inoculation. Functional classification revealed that those significantly differentially expressed circRNAs were associated with immune system process, rhythmic process and signaling following SE inoculation. CircRNAs NC_006091.4: 65510578|65515090, NC_006099.4: 16132825|16236906, and NC_006099.4: 15993284|16006290 play important roles in the response to SE inoculation. The findings in the current study provide evidence that circRNA alterations are involved in the response to SE inoculation in the chicken

No benefit of flat head positioning in early moderate-severe acute ischemic stroke: HeadPoST study subgroup analysis

Background Although the Head Positioning in acute Stroke Trial (HeadPoST) showed no effect of the flat head position (FP; vs sitting up head position (SUP)) on functional outcome, we hypothesised that it could still offer benefits if commenced early in those with acute ischaemic stroke (AIS) of at least moderate severity. Methods Subgroup analysis of HeadPoST in participants with National Institutes of Health Stroke Scale (NIHSS) scores ≥7, ≥10 and ≥14, randomised to FP or SUP <4.5 hours of AIS onset on functional outcomes defined by a shift in scores on the modified Rankin scale (mRS) and death/disability (mRS scores 3–6), and any cardiovascular serious adverse event. Logistic regression analyses were undertaken adjusted for study design and baseline risk factors. Results There was no significant differential treatment effect in patient subgroups defined by increasing baseline NIHSS scores: adjusted OR and 95% CI for ordinal shift and binary (3–6) mRS scores: for NIHSS ≥7 (n=867) 0.92 (0.67 to 1.25) and 0.74 (0.52 to 1.04); NIHSS ≥ 10 (n=606) 0.80 (0.58 to 1.10) and 0.77 (0.49 to 1.19); NIHSS ≥14 (n=378) 0.82 (0.54 to 1.24) and 1.22 (0.69 to 2.14). Conclusions Early FP had no significant effect in patients with moderate–severe AI

Prognostic significance of early urinary catheterization after acute stroke: Secondary analyses of the international HeadPoST trial

Background An indwelling urinary catheter (IUC) is often inserted to manage bladder dysfunction, but its impact on prognosis is uncertain. We aimed to determine the association of IUC use on clinical outcomes after acute stroke in the international, multi-center, cluster crossover, Head Positioning in Acute Stroke Trial (HeadPoST). Methods Data were analyzed on HeadPoST participants (n = 11,093) randomly allocated to the lying-flat or sitting-up head position. Binomial, logistic regression, hierarchical mixed models were used to determine associations of early insertion of IUC within seven days post-randomization and outcomes of death or disability (defined as “poor outcome,” scores 3–6 on the modified Rankin scale) and any urinary tract infection at 90 days with adjustment of baseline and post-randomization management covariates. Results Overall, 1167 (12%) patients had an IUC, but the frequency and duration of use varied widely across patients in different regions. IUC use was more frequent in older patients, and those with vascular comorbidity, greater initial neurological impairment (on the National Institutes of Health Stroke Scale), and intracerebral hemorrhage as the underlying stroke type. IUC use was independently associated with poor outcome (adjusted odds ratio (aOR): 1.40, 95% confidence interval (CI): 1.13–1.74), but not with urinary tract infection after adjustment for antibiotic treatment and stroke severity at hospital separation (aOR: 1.13, 95% CI: 0.59–2.18). The number exposed to IUC for poor outcome was 13. Conclusions IUC use is associated with a poor outcome after acute stroke. Further studies are required to inform appropriate use of IUC

Dysphagia screening and risks of pneumonia and adverse outcomes after acute stroke: An international multicenter study

Background Dysphagia is associated with aspiration pneumonia after stroke. Data are limited on the influences of dysphagia screen and assessment in clinical practice. Aims To determine associations between a “brief” screen and “detailed” assessment of dysphagia on clinical outcomes in acute stroke patients. Methods A prospective cohort study analyzed retrospectively using data from a multicenter, cluster cross-over, randomized controlled trial (Head Positioning in Acute Stroke Trial [HeadPoST]) from 114 hospitals in nine countries. HeadPoST included 11,093 acute stroke patients randomized to lying-flat or sitting-up head positioning. Herein, we report predefined secondary analyses of the association of dysphagia screening and assessment and clinical outcomes of pneumonia and death or disability (modified Rankin scale 3–6) at 90 days. Results Overall, 8784 (79.2%) and 3917 (35.3%) patients were screened and assessed for dysphagia, respectively, but the frequency and timing for each varied widely across regions. Neither use of a screen nor an assessment for dysphagia was associated with the outcomes, but their results were compared to “screen-pass” patients, those who failed had higher risks of pneumonia (adjusted odds ratio [aOR] = 3.00, 95% confidence interval [CI] = 2.18–4.10) and death or disability (aOR = 1.66, 95% CI = 1.41–1.95). Similar results were evidence for the results of an assessment for dysphagia. Subsequent feeding restrictions were related to higher risk of pneumonia in patients failed dysphagia screen or assessment (aOR = 4.06, 95% CI = 1.72–9.54). Conclusions Failing a dysphagia screen is associated with increased risks of pneumonia and poor clinical outcome after acute stroke. Further studies concentrate on determining the effective subsequent feeding actions are needed to improve patient outcomes

Genomic Polymorphism of the Pandemic A (H1N1) Influenza Viruses Correlates with Viral Replication, Virulence, and Pathogenicity In Vitro and In Vivo

The novel pandemic A (H1N1) virus was first identified in Mexico in April 2009 and quickly spread worldwide. Like all influenzas, the H1N1 strain-specific properties of replication, virulence, and pathogenicity are a result of the particular genomic sequence and concerted expression of multiple genes. Thus, specific mutations may support increased virulence and may be useful as biomarkers of potential threat to human health. We performed comparative genomic analysis of ten strains of the 2009 pandemic A (H1N1) influenza viruses to determine whether genotypes associated with clinical phenotypes, which ranged from mild to severe illness and up to lethal. Virus replication capacity was tested for each strain in vitro using cultured epithelial cells, while virulence and pathogenicity were investigated in vivo using the BALB/c mouse model. The results indicated that A/Sichuan/1/2009 strain had significantly higher replication ability and virulence than the other strains, and five unique non-synonymous mutations were identified in important gene-encoding sequences. These mutations led to amino acid substitutions in HA (L32I), PA (A343T), PB1 (K353R and T566A), and PB2 (T471M), and may be critical molecular determinants for replication, virulence, and pathogenicity. Our results suggested that the replication capacity in vitro and virulence in vivo of the 2009 pandemic A (H1N1) viruses were not associated with the clinical phenotypes. This study offers new insights into the transmission and evolution of the 2009 pandemic A (H1N1) virus