Miracle-dz/UniFAR-FTUs huggingface dataset:
High neutrophil to lymphocyte ratio in type A acute aortic dissection facilitates diagnosis and predicts worse outcome

Objective: The authors investigated whether neutrophil to lymphocyte ratio (N/L) can contribute to the diagnosis and risk assessment in patients with type A acute aortic dissection (AAD). Methods: The authors studied 120 consecutive patients with type A AAD (group I) and compared them with 121 consecutive patients with chronic aneurysms (group II) and 121 age- and sex-matched healthy subjects (group III). Result: It was found that white blood cell count, N/L, D-dimer and C-reactive protein were significantly higher in group I versus both groups II and III (p < 0.001 for all comparisons). White blood cell count and D-dimer were much higher in patients who died compared to survivors in group I (p = 0.023 and p = 0.033, respectively). A cutoff value of N/L >4.6 was associated with 0.89 sensitivity and 0.91 specificity for AAD. Conclusion: High N/L may contribute to the diagnostic evaluation and prompt immediate therapy in patients with type A AAD.
Preface on "pulmonary nodules special issue for lung cancer".

The incidence of small pulmonary nodules (SPNs) is increasing as a result of the widespread use of multislice spiral computed tomography (CT) and the low-dose helical CT screening for lung cancer (1). A pulmonary nodule is definite as a well or poorly-circumscribed, approximately spherical, radiographic opacity less than or equal to 30mm in diameter that is completely surrounded by aerated lung and is not associated with atelectasis, hilar enlargement, or pleural effusion, which can be divided into solid and sub-solid nodules, with the latter group further subdivided between pure ground-glass opacity (GGO) and part-solid nodules (2).
Clinical significance of ESR1 gene copy number changes in breast cancer as measured by fluorescence in situ hybridisation

Aims The ESR1 gene encodes for oestrogen receptor (ER) α, which plays a crucial role in mammary carcinogenesis and clinical outcome in patients with breast cancer. However, the clinical significance of the ESR1 gene copy number change for breast cancer has not been clarified. Methods ESR1 gene copy number was determined by fluorescence in situ hybridisation (FISH) on tissue sections. A minimum of 20 tumour cells were counted per section, and a FISH ratio of ESR1 gene to CEP6 ≥2.0 was considered ESR1 amplification. A ratio >1.2 but <2.0 was considered ESR1 gain. The ESR1 copy number was further measured by quantitative real-time PCR (Q-PCR) with ASXL2 as a reference. Results FISH revealed ESR1 amplification in six cases (4.0%) and ESR1 gain in 13 cases (8.7%) from a total of 150 cases. ESR1 gain and amplification were more common in older patients (p<0.001), and correlated well with ER protein expression (p=0.03) measured by immunohistochemistry, and ESR1 copy number (p<0.001) measured by Q-PCR. Furthermore, the multivariate analysis revealed that ESR1 amplification was associated with a shorter disease-free survival (HR=5.56, p=0.03) and a shorter overall survival (HR=5.11, p=0.04). Conclusions In general, the frequency of ESR1 amplification in breast cancer is low when measured by FISH in large sections. ESR1 gain and amplification in breast cancer may be associated with older age and poorer outcomes.
Mutational analysis of the Vibrio fischeri LuxI polypeptide: critical regions of an autoinducer synthase

Synthesis of the Vibrio fischeri autoinducer, a signal involved in the cell density-dependent activation of bioluminescence, is directed by the luxI gene product. The LuxI protein catalyzes the synthesis of N-acyl-homoserine lactones from S-adenosylmethionine and acylated-acyl carrier protein. We have gained an appreciation of the LuxI regions and amino acid residues involved in autoinducer synthesis by isolating and analyzing mutations generated by random and site-specific mutagenesis of luxI. By random mutagenesis we isolated 13 different single amino acid substitutions in the LuxI polypeptide. Eleven of these substitutions resulted in no detectable autoinducer synthase activity, while the remaining two amino acid substitutions resulted in reduced but detectable activity. The substitutions that resulted in no detectable autoinducer synthase activity mapped to two small regions of LuxI. In Escherichia coli, wild-type luxI showed dominance over all of the mutations. Because autoinducer synthesis has been proposed to involve formation of a covalent bond between an acyl group and an active-site cysteine, we constructed site-directed mutations that altered each of the three cysteine residues in LuxI. All of the cysteine mutants retained substantial activity as an autoinducer synthase in E. coli. Based on the analysis of random mutations we propose a model in which there are two critical regions of LuxI, at least one of which is an intimate part of an active site, and based on the analysis of site-directed mutations we conclude that an active-site cysteine is not essential for autoinducer synthase activity.
Das persönliche Pflanzenporträt – die Karde

Zusammenfassung Die Karde ist eine alte, traditionelle Heilpflanze, die ein breites Indikationsfeld aufweist. Die Traditionelle Chinesische Medizin verwendet sie schon lange, und auch in der abendländischen Volksheilkunde ist sie bekannt. Lange fand sie in der Literatur keine Erwähnung mehr und wurde erst in neuerer Zeit wiederentdeckt. Heute wird sie v. a. in der Erfahrungsmedizin zur Behandlung der Borreliose angewendet.
Age and Ethnic Differences in the Occurrence of Cervical Dysplasia, Cervical Cancer, and CervicalCancer Deaths in Suriname

Background: Updated information on the frequency of premalignant cervical lesions in Suriname is scant, while currently available data on the age and ethnic distribution of cervical dysplasia, cervical carcinoma, and cervical cancer deaths are inconsistent and conflicting. For these reasons, we assessed these topics using a retrospective cohort approach. Methods and Findings: Using secondary data, the incidence of cervical dysplasia (1995 - 2006) and cervical cancer (1980 - 2008), as well as cervical cancer mortality (1995 - 2010) was estimated and stratified per 10-year age groups and ethnic background. Data were evaluated for statistically significant differences using the Chi-square test and ANOVA, and expressed per 100,000 females per year. There were 2,554 records of dysplasia, 1, 117 for cervical carcinoma, and 283 for cervical cancer deaths during the indicated periods. The distribution of cervical dysplasia followed international patterns with a frequency of 1.7%for all lesions and for CIN1, CIN2 and CIN3/CIS of0.9, 0.5 and 0.3%, respectively. The average cervical cancer incidence was 24 per 100,000 women per year, and the average mortality rate was 10 per 100,000 women per year. The high-risk age groups for overall cervical dysplasia, cervical cancer, and mortality due to this disease were 30-49 (64-71%), 30-59 (60%), and 60-79 years (40%), respectively. Excess risk for cervical cancer and cervical cancer death was seen in Indigenous and Creole women. When compared to the other ethnic groups, Maroon women had the lowest cervical cancer incidence and mortality rates. Conclusions: Despite incomplete cancer registries, our data suggest that Suriname represents a high- risk country for cervical cancer; that current screening practices have a very limited impact on the incidence and mortality; and that high-risk groups are women aged 30-49 years and those of Indigenous and Creole background. These findings support the implementation of more targeted screening programs.
C4d-Positive Chronic Rejection: A Frequent Entity With a Poor Outcome

Background. Chronic rejection (CR) is an important cause of kidney graft loss. Some studies have suggested the role of antibodies mediating chronic graft dysfunction. In this context, C4d identification is an important tool to evaluate antibody-mediated rejection. Method. This is a retrospective study that analyzed 80 patients with histological diagnosis of chronic allograft nephropathy (CAN) according Banff 97 and no evidence of transplant glomerulopathy. These patients had renal biopsies available for C4d immunoperoxidase staining at the time of diagnosis. Cases were reclassified by the presence of C4d in peritubular capillaries. Results. C4d was negative in 30 cases (37.5%) and positive in 50 (62.5%). C4d+ group had more female and highly sensitized patients (PRA) at transplant. All variables were similar between C4d- and C4d+ cases at diagnosis time, but more C4d+ patients presented proteinuria (>0.3 g/L). Patients were submitted to various immunosuppression regimens after the CAN diagnosis. Four years after the diagnosis, death-censored graft survival was 87% for C4d- and 50% for C4d+ (P=0.002). In the multivariate Cox regression analysis, C4d+, PRA>10%, and vascular intimal proliferation were the variables that present higher relative risk for graft loss. Conclusion. These data indicate that C4d positive chronic rejection is very common, associated with proteinuria, and has a poor outcome. A larger study is warranted to identify which immunosuppressive regimen may modify the poor course of this entity.
Semi-invariants and their use for stability analysis of planar systems

Semi-invariants and relative characteristic functions extend to nonlinear systems the concept of eigenvector–eigenvalue pair for linear systems, and are, therefore, very useful to depict the behaviour of the system. In this article, semi-invariants are used to construct explicitly Lyapunov functions useful for studying the stability of the origin, for continuous-time systems. Moreover, using well-known tools from differential geometry such as (orbital) symmetries, it is shown how semi-invariants can be found for several classes of systems. Important connections with centre manifold theory are pointed out. By using the proposed general techniques, a new proof of a result claimed to Bendixson (Bendixson, I. (1901), ‘Sur les courbes définies par des équations différentielles’, Acta Mathematics, 24, 1–88) is given.
Persuasion with Motivated Beliefs

Considerable empirical research nds that people derive utility not only from consumption, but also from their beliefs about themselves and the world. Rather than dispassionately updating their views in response to new information, such belief-based utility implies that people at times avoid information and use other strategies to protect their existing beliefs. We present a two-stage model of persuasion in the presence of beliefprotecting strategies and test it in an incentive-compatible task. In the experiment, persuaders seek to shift receivers' subjective numeric estimates related to emotionally charged topics, such as abortion and racial discrimination. We manipulate whether the persuader rst acknowledges her own lack of certainty and whether she rst has an opportunity to build rapport with the receiver. Though these elements of communication ought to be irrelevant or even back re under the standard account, our theory predicts they will enhance persuasiveness. We nd that acknowledging doubt leads to a greater change in the receivers' beliefs, but nd no e ect for building rapport. Moreover, we nd that persuaders end up changing their own estimates after writing a persuasive message. Those who presented a strong argument (as judged by third party raters) end up revising their own estimate in the direction of their argument, while those who provided a weak argument update in the opposite direction.
A Conserved Leucine Zipper Motif in Gammaherpesvirus ORF52 Is Critical for Distinct Microtubule Rearrangements

ABSTRACT Productive viral infection often depends on the manipulation of the cytoskeleton. Herpesviruses, including rhesus monkey rhadinovirus (RRV) and its close homolog, the oncogenic human gammaherpesvirus Kaposi's sarcoma-associated herpesvirus/human herpesvirus 8 (KSHV/HHV8), exploit microtubule (MT)-based retrograde transport to deliver their genomes to the nucleus. Subsequently, during the lytic phase of the life cycle, the maturing viral particles undergo orchestrated translocation to specialized regions within the cytoplasm, leading to tegumentation, secondary envelopment, and then egress. As a result, we hypothesized that RRV might induce changes in the cytoskeleton at both early and late stages of infection. Using confocal imaging, we found that RRV infection led to the thickening and acetylation of MTs emanating from the MT-organizing center (MTOC) shortly after viral entry and more pronounced and diffuse MT reorganization during peak stages of lytic gene expression and virion production. We subsequently identified open reading frame 52 (ORF52), a multifunctional and abundant tegument protein, as being the only virally encoded component responsible for these cytoskeletal changes. Mutational and modeling analyses indicated that an evolutionarily conserved, truncated leucine zipper motif near the N terminus as well as a strictly conserved arginine residue toward the C terminus of ORF52 play critical roles in its ability to rearrange the architecture of the MT cytoskeleton. Taken together, our findings combined with data from previous studies describing diverse roles for ORF52 suggest that it likely binds to different cellular components, thereby allowing context-dependent modulation of function. IMPORTANCE A thorough understanding of the processes governing viral infection includes knowledge of how viruses manipulate their intracellular milieu, including the cytoskeleton. Altering the dynamics of actin or MT polymerization, for example, is a common strategy employed by viruses to ensure efficient entry, maturation, and egress as well as the avoidance of antiviral defenses through the sequestration of key cellular factors. We found that infection with RRV, a homolog of the human pathogen KSHV, led to perinuclear wrapping by acetylated MT bundles and identified ORF52 as the viral protein underlying these changes. Remarkably, incoming virions were able to supply sufficient ORF52 to induce MT thickening and acetylation near the MTOC, potentially aiding in the delivery viral genomes to the nucleus. Although the function of MT alterations during late stages of infection requires further study, ORF52 shares functional and structural similarities with alphaherpesvirus VP22, underscoring the evolutionary importance of MT cytoskeletal manipulations for this virus family.
Lack of selective Vβ deletion in CD4+ or CD8+ T lymphocytes and functional integrity of T‐cell repertoire during acute HIV syndrome

ObjectiveTo study the Vβ T-cell repertoire in peripheral blood lymphocytes (PBL) during acute HIV syndrome by using several anti-Vβ monoclonal antibodies (MAb) and to analyse its functionality by stimulating PBL with superantigens (SAg) such as Staphylococcus aureus enterotoxins. MethodsCytofluorimetric analysis of Vβ T-cell-receptor expression was performed on PBL from eight patients with symptomatic, acute HIV-1 primary infection, showing a dramatic decrease of CD4+ PBL accompanied by a marked increase in activated/memory CD8+ T cells, and on 12 age- and sex-matched healthy controls. PBL were then isolated, stimulated with different SAg, anti-CD3 MAb or phytohaemagglutinin and cultured for 3 days. PBL capability to progress through cell cycle was studied by the classic cytofluorimetric method of bromodeoxyuridine incorporation and DNA staining with propidium iodide. ResultsDespite the presence of a few expansions of some Vβ families among CD8+ T lymphocytes, no gross alterations in T-cell repertoire were present in patients with acute HIV syndrome. Its functionality was maintained overall, as PBL responsiveness to SAg was well preserved. Interestingly, all CD8+ T cells, although bearing different Vβ T-cell receptors, expressed marked signs of activation, i.e., CD45RO, CD38 and major histocompatibility complex class II molecules, and also high amounts of CD11a and CD18. ConclusionsOur data suggest, at least in the early phases and in the acute form of the infection, that HIV is not likely to act as a SAg. However, further studies are needed to analyse other sites, such as lymph nodes, where HIV could exert other, significant effects, and to study the expression of other Vβ families than those investigated here.
On the dielectric polarization effects in capacitive RF-MEMS switches

This paper investigates both theoretically and experimentally the dielectric charging effects of capacitive RF MEMS switches. Dielectric charging caused by charge injection under voltage stress was observed. The amphoteric nature of traps and its effect on the switch operation were confirmed under both positive and negative control voltages. Furthermore, it has been confirmed that the charging is a complicated process, which can be better described through the stretched exponential relaxation. This charging mechanism is the one that is responsible for the appearance of the negative pull out voltage and finally for the device failure.
Comparing direct and developmental encoding schemes in artificial evolution: a case study in evolving lens shapes

In this paper, different evolutionary encoding schemes were compared. In a simulator for geometrical optics different lens shapes in three dimensions were evolved using direct and indirect encodings. Direct and indirect methods were compared for their precision, convergence and efficiency. The results showed that the indirect encoding schemes converged faster than the direct ones, needed less genetic parameters and scientifically most important, it could be understood why the indirect scheme outperformed the direct one.
A DSP based real-time front car detection driving assistant system

This paper describes a lane recognition method for the front car detection and lane departure warning (FCD/LDW) system of smart vehicles and the algorithm implemented in a dual core ADI-BF561 600MHz DSP embedded system to verify the functionality. Since the computing power and memory size of the embedded system are not as good as those on a personal computer, special techniques have been applied in the algorithm to enhance the performance while maintain the reliability of the FCD/LDW results. Using the developed image recognition tools as the basis, the applied algorithm can detect front car in the same lane as well as the event of lane-departure. The distance from the detected front car can also be determined and alarms the warning to assist drivers for driving safety on the road. The system is implemented and tested on a DSP-based embedded platform which can perform the required processes in real-time under various weather conditions.
Endothelial dysfunction in dengue virus pathology

Dengue virus (DENV) is a leading cause of illness and death, mainly in the (sub)tropics, where it causes dengue fever and/or the more serious diseases dengue hemorrhagic fever and dengue shock syndrome that are associated with changes in vascular permeability. Despite extensive research, the pathogenesis of DENV is still poorly understood and, although endothelial cells represent the primary fluid barrier of the blood vessels, the extent to which these cells contribute to DENV pathology is still under debate. The primary target cells for DENV are dendritic cells and monocytes/macrophages that release various chemokines and cytokines upon infection, which can activate the endothelium and are thought to play a major role in DENV‐induced vascular permeability. However, recent studies indicate that DENV also replicates in endothelial cells and that DENV‐infected endothelial cells may directly contribute to viremia, immune activation, vascular permeability and immune targeting of the endothelium. Also, the viral non‐structural protein‐1 and antibodies directed against this secreted protein have been reported to be involved in endothelial cell dysfunction. This review provides an extensive overview of the effects of DENV infection on endothelial cell physiology and barrier function. Copyright © 2014 John Wiley & Sons, Ltd.
RGB-D depth-map restoration using smooth depth neighborhood supports

Abstract. A method to restore the depth map of an RGB-D image using smooth depth neighborhood (SDN) supports is presented. The SDN supports are computed based on the corresponding color image of the depth map. Compared with the most widely used square supports, the proposed SDN supports can well-capture the local structure of the object. Only pixels with similar depth values are allowed to be included in the support. We combine our SDN supports with the joint bilateral filter (JBF) to form the SDN-JBF and use it to restore depth maps. Experimental results show that our SDN-JBF can not only rectify the misaligned depth pixels but also preserve sharp depth discontinuities.
Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides

We have improved upon the methodology and dramatically shortened the time required for accurate assembly of 5- to 6-kb segments of DNA from synthetic oligonucleotides. As a test of this methodology, we have established conditions for the rapid (14-day) assembly of the complete infectious genome of bacteriophage φX174 (5,386 bp) from a single pool of chemically synthesized oligonucleotides. The procedure involves three key steps: (i) gel purification of pooled oligonucleotides to reduce contamination with molecules of incorrect chain length, (ii) ligation of the oligonucleotides under stringent annealing conditions (55°C) to select against annealing of molecules with incorrect sequences, and (iii) assembly of ligation products into full-length genomes by polymerase cycling assembly, a nonexponential reaction in which each terminal oligonucleotide can be extended only once to produce a full-length molecule. We observed a discrete band of full-length assemblies upon gel analysis of the polymerase cycling assembly product, without any PCR amplification. PCR amplification was then used to obtain larger amounts of pure full-length genomes for circularization and infectivity measurements. The synthetic DNA had a lower infectivity than natural DNA, indicating approximately one lethal error per 500 bp. However, fully infectious φX174 virions were recovered after electroporation into Escherichia coli. Sequence analysis of several infectious isolates verified the accuracy of these synthetic genomes. One such isolate had exactly the intended sequence. We propose to assemble larger genomes by joining separately assembled 5- to 6-kb segments; ≈60 such segments would be required for a minimal cellular genome.
The Time of Prenatal Immune Challenge Determines the Specificity of Inflammation-Mediated Brain and Behavioral Pathology

Disturbance to early brain development is implicated in several neuropsychiatric disorders including autism, schizophrenia, and mental retardation. Epidemiological studies have indicated that the risk of developing these disorders is enhanced by prenatal maternal infection, presumably as a result of neurodevelopmental defects triggered by cytokine-related inflammatory events. Here, we demonstrate that the effects of maternal immune challenge between middle and late gestation periods in mice are dissociable in terms of fetal brain cytokine responses to maternal inflammation and the pathological consequences in brain and behavior. Specifically, the relative expression of pro- and anti-inflammatory cytokines in the fetal brains in response to maternal immune challenge may be an important determinant among other developmental factors for the precise pathological profile emerging in later life. Thus, the middle and late gestation periods correspond to two windows with differing vulnerability to adult behavioral dysfunction, brain neuropathology in early adolescence, and of the acute cytokine responses in the fetal brain.