Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth form evolution and shifting habitat specialization in annual plants

Optimal plant growth form should vary across environments. We examined the potential for mutations causing large changes in growth form to produce new optimal phenotypes across light environments. We predicted that the upright growth form would be favoured in a light limiting environment as leaves were in a position to maximize light interception, while a rosette (leaves in a basal position) growth form would be favoured in a high light environment. Growth form genotypes of Brassica rapa (upright wild‐type and rosette mutants) and Arabidopsis thaliana (large rosette wild‐type and increasingly upright growth form mutants) were grown in a greenhouse in control (ambient) and filtered (low) light treatments. Compared to upright genotypes, rosette genotypes had relatively high fitness in control light but had a relatively large fitness reduction in filtered light. Our results demonstrate the potential importance of rapid growth form evolution in plant adaptation to new or changing environments.
Eindhoven University of Technology MASTER A simulation study on the impact of RFID technologies applied to in-store inventory management processes subject to shrinkage delivery and transaction errors

Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration.
HIV-1 Vpu Antagonism of Tetherin Inhibits Antibody-Dependent Cellular Cytotoxic Responses by Natural Killer Cells

ABSTRACT The type I interferon-inducible factor tetherin retains virus particles on the surfaces of cells infected with vpu-deficient human immunodeficiency virus type 1 (HIV-1). While this mechanism inhibits cell-free viral spread, the immunological implications of tethered virus have not been investigated. We found that surface tetherin expression increased the antibody opsonization of vpu-deficient HIV-infected cells. The absence of Vpu also stimulated NK cell-activating FcγRIIIa signaling and enhanced NK cell degranulation and NK cell-mediated antibody-dependent cellular cytotoxicity (ADCC). The deletion of vpu in HIV-1-infected primary CD4+ T cells enhanced the levels of antibody binding and Fc receptor signaling mediated by HIV-positive-patient-derived antibodies. The magnitudes of antibody binding and Fc signaling were both highly correlated to the levels of tetherin on the surfaces of infected primary CD4 T cells. The affinity of antibody binding to FcγRIIIa was also found to be critical in mediating efficient Fc activation. These studies implicate Vpu antagonism of tetherin as an ADCC evasion mechanism that prevents antibody-mediated clearance of virally infected cells. IMPORTANCE The ability of the HIV-1 accessory factor to antagonize tetherin has been considered to primarily function by limiting the spread of virus by preventing the release of cell-free virus. This study supports the hypothesis that a major function of Vpu is to decrease the recognition of infected cells by anti-HIV antibodies at the cell surface, thereby reducing recognition by antibody-dependent clearance by natural killer cells.
Participatory design workshops with children with cancer: lessons learned

The design and development of information technology for use in health services presents a complex and sensitive situation. It includes not only managing differing interests and situations, but does so in a context that might give rise to negative emotions among the participating users. When the future users are children, this design process becomes even more complex. Participatory design is considered suitable for design with children. The premise for the participation of the children in this study was that they were, or had been treated for cancer. Therefore, their participation could awaken negative emotions, and make the situation difficult for them to handle. How participatory design with children can be conducted in such a sensitive context is therefore explored, grounded in the experience from six design workshops. The workshops evolved around the concept of comics as a way to allow the children to express themselves with familiar means. Three main lessons were learned from the workshops: working in pairs promotes an efficient work situation and the possibility to keep an eye on the children's wellbeing; proxies need to be distanced from the participating children; and the scenarios in the comics set the level of realism of the result.
Prone positioning in patients with moderate and severe acute respiratory distress syndrome: a randomized controlled trial.

CONTEXT Post hoc analysis of a previous trial has suggested that prone positioning may improve survival in patients with severe hypoxemia and with acute respiratory distress syndrome (ARDS). OBJECTIVE To assess possible outcome benefits of prone positioning in patients with moderate and severe hypoxemia who are affected by ARDS. DESIGN, SETTING, AND PATIENTS The Prone-Supine II Study, a multicenter, unblinded, randomized controlled trial conducted in 23 centers in Italy and 2 in Spain. Patients were 342 adults with ARDS receiving mechanical ventilation, enrolled from February 2004 through June 2008 and prospectively stratified into subgroups with moderate (n = 192) and severe (n = 150) hypoxemia. INTERVENTIONS Patients were randomized to undergo supine (n = 174) or prone (20 hours per day; n = 168) positioning during ventilation. MAIN OUTCOME MEASURES The primary outcome was 28-day all-cause mortality. Secondary outcomes were 6-month mortality and mortality at intensive care unit discharge, organ dysfunctions, and the complication rate related to prone positioning. RESULTS Prone and supine patients from the entire study population had similar 28-day (31.0% vs 32.8%; relative risk [RR], 0.97; 95% confidence interval [CI], 0.84-1.13; P = .72) and 6-month (47.0% vs 52.3%; RR, 0.90; 95% CI, 0.73-1.11; P = .33) mortality rates, despite significantly higher complication rates in the prone group. Outcomes were also similar for patients with moderate hypoxemia in the prone and supine groups at 28 days (25.5% vs 22.5%; RR, 1.04; 95% CI, 0.89-1.22; P = .62) and at 6 months (42.6% vs 43.9%; RR, 0.98; 95% CI, 0.76-1.25; P = .85). The 28-day mortality of patients with severe hypoxemia was 37.8% in the prone and 46.1% in the supine group (RR, 0.87; 95% CI, 0.66-1.14; P = .31), while their 6-month mortality was 52.7% and 63.2%, respectively (RR, 0.78; 95% CI, 0.53-1.14; P = .19). CONCLUSION Data from this study indicate that prone positioning does not provide significant survival benefit in patients with ARDS or in subgroups of patients with moderate and severe hypoxemia. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00159939.
Four novel ELANE mutations in patients with congenital neutropenia

Congenital neutropenia is a heterogeneous bone marrow failure syndrome characterized by a maturation arrest of myelopoesis at the promyelocyte/myelocyte stage. Cyclic neutropenia (CyN) and severe congenital neutropenia (SCN) are two main forms of congenital neutropenia. Genetic analysis has shown that heterozygous mutations in the ELANE gene encoding the neutrophil elastase are the major cause of these disorders. We investigated the prevalence of ELANE mutations in a group of 16 patients from 14 families with congenital neutropenia. Five patients had typical manifestations of CyN, and 11 patients had SCN. Seven different heterozygous ELANE mutations were found, including four novel mutations. Pediatr Blood Cancer 2011; 57: 332–335. © 2011 Wiley‐Liss, Inc.
Squeeze film lubrication in piston rings and reciprocating contacts

A detailed analysis of ‘squeeze’ lubrication effects in piston rings and reciprocating line contacts is reported. Inclusion of ‘squeeze’ effects leads to significant oil film thicknesses at reversal positions, and the pressure distribution in the lubricated contact can extend over the full face of the contact, whereas in models which neglect ‘squeeze’ effects, oil film thicknesses are predicted to be zero at reversal positions, and only half the contact is wetted. If it is desired to reduce friction losses without affecting durability, it is shown that one interesting ‘co-engineering’ option would be to use a lower viscosity lubricant, and at the same time, use ‘flatter’ piston rings. This is shown to lead to both lower friction and higher oil minimum film thicknesses. The model developed for piston rings can be applied to reciprocating line contacts with very little modification, and once again, it is found that the inclusion of ‘squeeze’ effects has a significant impact on oil film thickness, and it is also shown that the friction force is different dependent on the direction of sliding of the contact.
Impact of Multiple Factors on the Degree of Tinnitus Distress

Objective: The primary cause of subjective tinnitus is a dysfunction of the auditory system; however, the degree of distress tinnitus causes depends largely on the psychological status of the patient. Our goal was to attempt to associate the grade of tinnitus-related distress with the psychological distress, physical, or psychological discomfort patients experienced, as well as potentially relevant social parameters, through a simultaneous analysis of these factors. Methods: We determined the level of tinnitus-related distress in 531 tinnitus patients using the German version of the tinnitus questionnaire (TQ). In addition, we used the Perceived Stress Questionnaire (PSQ); General Depression Scale Allgemeine Depression Skala (ADS), Berlin Mood Questionnaire (BSF); somatic symptoms inventory (BI), and SF-8 health survey as well as general information collected through a medical history. Results: The TQ score significantly correlated with a score obtained using PSQ, ADS, BSF, BI, and SF-8 alongside psychosocial factors such as age, gender, and marital status. The level of hearing loss and the auditory properties of the specific tinnitus combined with perceived stress and the degree of depressive mood and somatic discomfort of a patient were identified as medium-strong predictors of chronic tinnitus. Social factors such as gender, age, or marital status also had an impact on the degree of tinnitus distress. The results that were obtained were implemented in a specific cortical distress network model. Conclusions: Using a large representative sample of patients with chronic tinnitus permitted a simultaneous statistical measurement of psychometric and audiological parameters in predicting tinnitus distress. We demonstrate that single factors can be distinguished in a manner that explains their causative association and influence on the induction of tinnitus-related distress.
Comparative studies on the functional roles of N‐ and C‐terminal regions of molluskan and vertebrate troponin‐I

Vertebrate troponin regulates muscle contraction through alternative binding of the C‐terminal region of the inhibitory subunit, troponin‐I (TnI), to actin or troponin‐C (TnC) in a Ca2+‐dependent manner. To elucidate the molecular mechanisms of this regulation by molluskan troponin, we compared the functional properties of the recombinant fragments of Akazara scallop TnI and rabbit fast skeletal TnI. The C‐terminal fragment of Akazara scallop TnI (ATnI232−292), which contains the inhibitory region (residues 104–115 of rabbit TnI) and the regulatory TnC‐binding site (residues 116–131), bound actin‐tropomyosin and inhibited actomyosin‐tropomyosin Mg‐ATPase. However, it did not interact with TnC, even in the presence of Ca2+. These results indicated that the mechanism involved in the alternative binding of this region was not observed in molluskan troponin. On the other hand, ATnI130−252, which contains the structural TnC‐binding site (residues 1–30 of rabbit TnI) and the inhibitory region, bound strongly to both actin and TnC. Moreover, the ternary complex consisting of this fragment, troponin‐T, and TnC activated the ATPase in a Ca2+‐dependent manner almost as effectively as intact Akazara scallop troponin. Therefore, Akazara scallop troponin regulates the contraction through the activating mechanisms that involve the region spanning from the structural TnC‐binding site to the inhibitory region of TnI. Together with the observation that corresponding rabbit TnI‐fragment (RTnI1−116) shows similar activating effects, these findings suggest the importance of the TnI N‐terminal region not only for maintaining the structural integrity of troponin complex but also for Ca2+‐dependent activation.
Plasma Prolidase Activity and Oxidative Stress in Patients with Parkinson's Disease

Prolidase deficiency has been related to mental retardation and oxidative stress. The study aimed to observe plasma prolidase activity (PPA), total oxidant status (TOS), total antioxidant status (TAS), and oxidative stress index (OSI) in patients with Parkinson's disease (PD). 240 subjects with PD and 150 healthy volunteers were considered as cases and controls, respectively. PPA, TOS, TAS, and OSI were measured spectrophotometrically. PPA and TAS in cases were more significantly decreased than controls (P < 0.01), while TOS and OSI were significantly increased (P < 0.001). In cases, nonsignificant, positive correlation was observed between PPA and TOS and OSI while significant, negative correlation was observed between PPA and TAS (P = 0.047). PPA in cases was nonsignificantly decreased with increased duration of PD (P = 0.747) while TAS was significantly decreased (P < 0.001) and TOS and OSI were significantly increased (P < 0.001). It was observed that higher age groups had decreased PPA, and TAS and increased TOS and OSI compared to lower age groups in cases. In summary, patients with PD have decreased PPA and increased oxidative stress compared to healthy volunteers. PPA was associated with oxidative stress markers in patients with PD. Decreased PPA and TAS and increased TOS and OSI were associated with progression of disease and higher age.
Correspondence Autoencoders for Cross-Modal Retrieval

This article considers the problem of cross-modal retrieval, such as using a text query to search for images and vice-versa. Based on different autoencoders, several novel models are proposed here for solving this problem. These models are constructed by correlating hidden representations of a pair of autoencoders. A novel optimal objective, which minimizes a linear combination of the representation learning errors for each modality and the correlation learning error between hidden representations of two modalities, is used to train the model as a whole. Minimizing the correlation learning error forces the model to learn hidden representations with only common information in different modalities, while minimizing the representation learning error makes hidden representations good enough to reconstruct inputs of each modality. To balance the two kind of errors induced by representation learning and correlation learning, we set a specific parameter in our models. Furthermore, according to the modalities the models attempt to reconstruct they are divided into two groups. One group including three models is named multimodal reconstruction correspondence autoencoder since it reconstructs both modalities. The other group including two models is named unimodal reconstruction correspondence autoencoder since it reconstructs a single modality. The proposed models are evaluated on three publicly available datasets. And our experiments demonstrate that our proposed correspondence autoencoders perform significantly better than three canonical correlation analysis based models and two popular multimodal deep models on cross-modal retrieval tasks.
Comparing the Nambu-Goto string with LGT results

We discuss a way to evaluate the full prediction for the interquark potential which is expected from the effective Nambu-Goto string model. We check the correctness of the prescription reproducing the results obtained with the zeta function regularization for the first two perturbative orders. We compare the predictions with existing Monte Carlo data for the (2+1) dimensional Z(2), SU(2) and SU(3) gauge theories: in the low temperature regime, we find good agreement for large enough interquark distances, but an increasing mismatch between theoretical predictions and numerical results is observed as shorter and shorter distances are investigated. On the contrary, at high temperatures (approaching the deconfinement transition from below) a remarkable agreement between Monte Carlo data and the expectations from the Nambu-Goto effective string is observed for a wide range of interquark distances.
Climatic Gradients of Arms Race Coevolution

In nature, spatiotemporally dynamic coevolutionary processes play major roles in the foundation and maintenance of biodiversity. Here, we examined the arms race coevolution involving a seed-eating weevil with a long snout and its camellia plant host with a thick fruit coat (pericarp) throughout the marked climatic gradient observed across the Japanese islands. Results demonstrated that female weevils, which bored holes through camellia pericarps to lay eggs into seeds, had evolved much longer snouts than males, especially in areas in which Japanese camellia pericarps were very thick. The thickness of the plant pericarp was heritable, and the camellia plant evolved a significantly thicker pericarp on islands with the weevil than on islands without it. Across populations with weevils, resource allocation to plant defense increased with increasing annual mean temperature or annual precipitation, thereby geographically differentiating the evolutionary and ecological interactions between the two species. Given that the coevolutionary relationship exhibited appreciable variation across a relatively small range of annual mean temperatures, ongoing global climatic change can dramatically alter the coevolutionary process, thereby changing the ecological interaction between these species.
Variations of high frequency parameter of heart rate variability following osteopathic manipulative treatment in healthy subjects compared to control group and sham therapy: randomized controlled trial

Context: Heart Rate Variability (HRV) indicates how heart rate changes in response to inner and external stimuli. HRV is linked to health status and it is an indirect marker of the autonomic nervous system (ANS) function. Objective: To investigate the influence of osteopathic manipulative treatment (OMT) on cardiac autonomic modulation in healthy subjects, compared with sham therapy and control group. Methods: Sixty-six healthy subjects, both male and female, were included in the present 3-armed randomized placebo controlled within subject cross-over single blinded study. Participants were asymptomatic adults (26.7 ± 8.4 y, 51% male, BMI 18.5 ± 4.8), both smokers and non-smokers and not on medications. At enrollment subjects were randomized in three groups: A, B, C. Standardized structural evaluation followed by a patient need-based osteopathic treatment was performed in the first session of group A and in the second session of group B. Standardized evaluation followed by a protocoled sham treatment was provided in the second session of group A and in the first session of group B. No intervention was performed in the two sessions of group C, acting as a time-control. The trial was registered on clinicaltrials.gov identifier: NCT01908920. Main Outcomes Measures: HRV was calculated from electrocardiography before, during and after the intervention, for a total amount time of 25 min and considering frequency domain as well as linear and non-linear methods as outcome measures. Results: OMT engendered a statistically significant increase of parasympathetic activity, as shown by High Frequency power (p < 0.001), expressed in normalized and absolute unit, and possibly decrease of sympathetic activity, as revealed by Low Frequency power (p < 0.01); results also showed a reduction of Low Frequency/High Frequency ratio (p < 0.001) and Detrended fluctuation scaling exponent (p < 0.05). Conclusions: Findings suggested that OMT can influence ANS activity increasing parasympathetic function and decreasing sympathetic activity, compared to sham therapy and control group.
Omega-3 Polyunsaturated Fatty Acids in the Treatment of Non-Alcoholic FattyLiver Disease: Are They So Good?

Non-alcoholic fatty liver disease (NAFLD) is the most prevalent hepatic problem in Western and Asian countries where it can affect more than 30% of people [1]. NAFLD pathological characteristic is a fat infiltration of the hepatocytes (hepatic steatosis) in subjects who are mild or no alcohol drinkers and do not have other secondary causes of hepatic lipid accumulation. In one fifth of affected patients, NAFLD can evolve in a liver inflammatory damage, which is associated with oxidative stress, cytolysis, and fibrosis (steatohepatitis) [2]. Of these patients, more than one-third progress to liver cirrhosis and a small part can develop hepatocarcinoma along years. It’s not clear why some patients with NAFLD evolve to non-alcoholic steatohepatitis (NASH) while others remain stable over years, though a role of intestinal inflammation, gut dysbiosis, and hypovitaminosis D has been recently proposed [3]. Consistently, subjects at high risk to develop NAFLD are those affected by obesity, type 2 diabetes mellitus, and other conditions associated with insulin resistance or hyperinsulinemia such as hypertension, dyslipidemia, polycystic ovary disease, and metabolic syndrome, as well as patients with chronic inflammatory bowel diseases [4]. Patients with NAFLD are characterized by increased circulatory levels of triglycerides and free fatty acids (FFAs) that come from the adipose tissue through the lipolytic process, from the hepatic lipid de-novo synthesis, and to a minor extent from food intake. Both insulin resistance and hyperinsulinemia in predisposed subjects are associated with a visceral fat distribution and are responsible for the high level of circulatory FFAs [5]. FFAs enter and accumulate in insulin-resistant hepatocytes and by esterification with glycerol increase hepatic triglycerides synthesis and very low-density lipoproteins (VLDL) production; thus, favoring hypertriglyceridemia. The overflow of plasma lipids and lipid metabolites in non-adipose tissues induces “lipotoxicity”, a pathological process characterized by lipids accumulation in liver and in other organs such as heart, kidney, pancreas, and skeletal muscle [6]. This process is responsible for the development and progression of heart and kidney failure, obesity, and diabetes, as well as for the systemic release of inflammatory cytokines. System cytokines maintain chronic subclinical inflammation, induce oxidative stress and endothelial dysfunction, and predispose to the atherosclerotic process [7]. Although NAFLD has been considered as the hepatic manifestation of the metabolic syndrome, evidence has shown that NAFLD is associated with cardiovascular morbidity and mortality independently of metabolic syndrome. Therefore, other than pro-cirrhotic, NAFLD had to be considered an important modifiable risk factor for cardiovascular diseases [8].