Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of a new photoresist (DiaPlate 133) with SU-8 using both x-ray and ion beam lithographies

We describe essentially the lithography performed on a new photoresist, called DiaPlate 133. This negative resin has been structured by an x-ray beam produced by a new high brightness synchrotron light source, the Swiss Light Source (SLS) located at Villigen, near Zurich, during a 8 h-run and compared with another well-known resin, SU-8. Then the resins have been structured with ions at CAFI and both techniques are compared. Results and comments are presented underneath. It can be noted that the x-ray and ion beam lithography tests we performed with DiaPlate 133 were the first ones ever realized.
Metals in Alzheimer's Disease: A Combined Experimental and Numerical Approach

Alzheimer disease is a pathology causing severe problems with memory, thinking and behavior. It accounts for the majority of dementia cases and is the sixth leading cause of death in developed countries. Unfortunately a real cure is still missing and the drug treatments today available can only reduce symptoms. It belongs to a large class of diseases, called amyloidosis, in which endogenous proteins or peptides undergo a misfolding process switching from the physiological soluble configuration to a pathological fibrillar insoluble state. An important, but not yet fully elucidated, role appears to be played in these processes by transition metals (mainly copper and zinc) that have been observed to be present in fairly large amounts in patient's neurological plaques. In this review we will show that the challenging problem of understanding the physico-chemical basis of protein misfolding and aggregation can be successfully investigated with a combination of modern spectroscopic techniques and advanced first principle numerical simulations. In particular, it will be shown that different metals can rival in peptide binding thus adding support to the hypothesis that metal dyshomeostasis may be relevant in the Alzheimer disease development.
Identification of conserved slow codons that are important for protein expression and function

ABSTRAST Due to the redundancy of the genetic code most amino acids are encoded by several ‘synonymous‘ codons. These codons are used unevenly, and each organism demonstrates its own unique codon usage bias, where the ‘preferred’ codons are associated with tRNAs that are found in high concentrations. Therefore, for decades, the prevailing view had been that preferred and non-preferred codons are linked to high or slow translation rates, respectively. However, this simplified view is contrasted by the frequent failures of codon-optimization efforts and by evidence of non-preferred (i.e. ‘slow’) codons having specific roles important for efficient production of functional proteins. One such specific role of slower codons is the regulation of co-translational protein folding, a complex biophysical process that is very challenging to model or to measure. Here, we combined a genome-wide approach with experiments to investigate the role of slow codons in protein production and co-translational folding. We analysed homologous gene groups from divergent bacteria and identified positions of inter-species conservation of bias towards slow codons. We then generated mutants where the conserved slow codons are substituted with ‘fast’ ones, and experimentally studied the effects of these codon substitutions. Using cellular and biochemical approaches we find that at certain locations, slow-to-fast codon substitutions reduce protein expression, increase protein aggregation, and impair protein function. This report provides an approach for identifying functionally relevant regions with slower codons and demonstrates that such codons are important for protein expression and function.
Treatment of Essential Thrombocythemia with Anagrelide Is Associated with an Increased Risk of Worsened Kidney Function

Background and Purpose: When choosing a cytoreduction method for patients suffering from essential thrombocythemia (ET), it is important to know the safety profile of the medicine used. Few articles have been published about the effects of hydroxycarbamide (hydroxyurea, HU) and anagrelide (ANA) on renal function in ET patients. This study is the largest analysis of nephrotoxicity of cytoreductive drugs used in ET therapy so far, which additionally includes risk factors for the progression of kidney disease and coexisting genetic mutation. Experimental Approach: The retrospective study included 310 patients diagnosed with ET. Demographic data, comorbidities, Cr, and estimated glomerular filtration rate (eGFR) were all taken into account prior to diagnosis and after 6 months of HU and ANA treatment. Key Results: A statistically significant difference was found between Cr and eGFR levels at baseline and after 6 months of treatment (p < 0.001). The applied treatment (HU and ANA) had the greatest impact on kidney function. ANA significantly increased the risk of worsening renal function in contrary to hydroxycarbamide after 6 months of treatment (eGFR change: median +1 mL/min/1.73 m2 [interquartile range (IQR) (−4)–(+7)] in the HU group vss. median −13 mL/min/1.73 m2 [IQR (−18)–(−6)] in the ANA group, odds ratio [OR] 7.92 95% confidence interval [95% CI] [4.17–15.08], p < 0.001). Lowering of eGFR <60 mL/min/1.73 m2 occurred in 31 patients (31.0%) from the ANA group and 10 people (4.8%) treated with HU (p = 0.000). In 1 patient from the ANA group, >50% decrease in eGFR was observed. The chance for an increase in Cr levels was higher in people with pre-existing arterial hypertension (OR 1.92 CI = 95% [1.21–3.05], p = 0.006). Sex, type of mutation found (JAK2 V617F or CALR), and previous renal impairment did not affect renal function after 6 months of treatment. In addition, there was no difference in the efficacy of ET treatment between HU and ANA (p = 0.998). Conclusions and Implications: The observations indicate that ANA should be used in patients with ET with great caution and taking into account the risk of worsened kidney function.
Application of multilayer perceptron neural networks for predicting the permeability tensor components of thin ferrite films

A novel characterization method using artificial neural networks is presented. This method allows one to determine the intrinsic permeability tensor of ferrite thin-films from S -parameters measurements. Neural networks, efficient to solve inverse problems, are used to compute the permeability tensor components μ and k. This optimization technique is used to find extremely complex functions between inputs and outputs and can be successfully applied on our magnetic thin-film characterization problem. Results of our networks are compared to a theoretical model. A great number of both simulated and measured tests have been performed on many magnetic thin-films. Neural network processing leads to a rapid and robust method for predicting the magnetic characterization of thin-films in microwave range.
Wide Diurnal Temperature Amplitude and High Population Density Can Positively Affect the Life History of Sitobion avenae (Hemiptera: Aphididae)

Abstract Diurnal temperature amplitude is known to have a large influence on insect life history. Population density affects intraspecific competition and many other aspects of insect life history. However, there is limited information on the interactive effects of these factors on insects. Here, we tested the interactive effects of three diurnal temperature amplitudes (22 ± 0°C, 22 ± 6°C, and 22 ± 12°C) and three population densities on the development, survival, longevity, and fecundity of the English grain aphid Sitobion avenae (Fabricius) (Homoptera: Aphididae). At a constant temperature, increasing population density reduced the growth and survival of early-instar nymphs, increased longevity, and reduced fecundity. At a low population density, increasing temperature amplitude inhibited nymph development. However, even at a high temperature amplitude, nymph survival rate was higher than expected, and reproduction was possible because the recovery of the lower night-temperatures eliminated thermal stress. Increasing the population density reduced, and even reversed, the negative effects of the wide temperature amplitude. This may reflect synergistic interactions between population density and wide temperature amplitude as these stressors each incur energetic costs. These findings emphasize the importance of temperature amplitude and population density for improving prediction accuracy and damage assessment during pest control modeling.
Understanding the Improved Electrochemical Performances of Fe-Substituted 5 V Spinel Cathode LiMn1.5Ni0.5O4

Partial substitution of Fe for Ni alone or both for Ni and Mn in the 5 V spinel cathode LiMn1.5Ni0. 5O4 has been investigated by characterizing the samples by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), charge−discharge measurements in lithium cells, electrochemical impedance spectroscopy (EIS), chronoamperometry (CA), and X-ray photoelectron spectroscopy (XPS). The Fe-substituted samples exhibit remarkably superior cycling performances and higher rate capabilities than the pristine LiMn1.5Ni0. 5O4. The greatly enhanced electrochemical performances by the Fe substitution are attributed to the (i) stabilization of the structure with cation-disorder in the 16d octahedral sites of the spinel lattice, (ii) suppression of the formation of a thick solid-electrolyte interfacial (SEI) layer due to the Fe-enrichment and Ni-deficiency on the surface, (iii) production of Mn3+ and the consequent enhancement in electronic conductivity, and (iv) much reduced polarization loss arising from bo.
Diagnosis of solid tumors in infants by fine‐needle aspiration cytology: 5 years retrospective study from a tertiary care oncology center in South India

Neuroblastoma (NB), Wilms tumor (WT), hepatoblastoma (HBL), germ cell tumors (GCT), rhabdomyosarcoma (RMS), and so forth are the commonly identified solid tumors in infants. Invasive diagnostic techniques are more challenging in infants than older children. fine needle aspiration cytology (FNAC) is a safe, minimally invasive and outpatient procedure which is time and cost‐effective for solid tumor diagnosis. This study aims to evaluate the role of FNAC in the diagnosis of various infantile solid tumors.
Clinical utility of the GAD-7 in identifying anxiety disorders after traumatic brain injury

ABSTRACT To determine if the GAD-7 provides incremental value, predicting a final diagnosis of an anxiety disorder after traumatic brain injury (TBI). Retrospective analysis of archival data of 100 patients with TBI, who underwent neuropsychological evaluation 1–12 months after injury. Receiver Operating Characteristic analysis determined the optimal cutoff point for clinically significant symptoms on the GAD−7. Hierarchical logistic regression analyses determined the relative contributions of premorbid psychiatric history, injury severity, and GAD−7 results in predicting a final diagnosis of anxiety disorder. GAD−7 cutoff point of ≥7 yielded the best combination of sensitivity and specificity regarding a final diagnosis of anxiety disorder. Within hierarchical logistic regression models, injury severity did not statistically significantly add to prior psychiatric history in predicting a final diagnosis of anxiety disorder. When GAD-7 was added, it made a statistically significant contribution in accounting for such a diagnosis and increased sensitivity from 71% to 91%. The GAD−7 holds diagnostic utility as a screening measure for anxiety disorders in patients with TBI. It should not be used in isolation but as part of a more comprehensive interview and history. The GAD−7 can benefit clinicians in assisting with timelier identification and treatment of symptoms of anxiety.
Use of Genetic Algorithms and Artificial Neural Networks to Predict the Resolution of Amino Acids in Thin-Layer Chromatography

A novel method is proposed for optimization of simultaneous thinlayer chromatographic separation of seven amino acids. For this purpose we used a useful combination of genetic algorithms (GA) with artificial neural networks (ANN). Methods investigated in this work were successfully used for prediction of resolution (RS) and optimization of the thin-layer chromatographic separation of model solutions containing the seven compound. Very good correlation was achieved between predicted and calculated RS data, and low absolute and relative errors were obtained.
Organic aerosol components observed in worldwide datasets from aerosol mass spectrometry

N. L. Ng, M. R. Canagaratna, Q. Zhang, J. L. Jimenez, J. Tian, I. M. Ulbrich, J. H. Kroll, K. S. Docherty, P. S. Chhabra, R. Bahreini, S. M. Murphy, J. H. Seinfeld, L. Hildebrandt, P. F. DeCarlo, V. A. Lanz, A. S. H. Prevot, E. Dinar, Y. Rudich, and D. R. Worsnop Aerodyne Research, Inc. Billerica, MA, USA Atmospheric Sciences Research Center, State University of New York, Albany, NY, USA CIRES, University of Colorado, Boulder, CO, USA Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA Department of Chemical Engineering, California Institute of Technology, Pasadena, CA, USA NOAA, Earth System Research Laboratory, Boulder, CO, USA Center for Atmospheric Particle Studies, Carnegie Mellon University, Pittsburgh, PA, USA Department of Atmospheric and Oceanic Science, University of Colorado, Boulder, CO, USA
What are the factors affecting the progression of kidney failure, mortality and morbidity after cardiac surgery in patients with chronic kidney disease?

Acute kidney injury occurs in as many as 40% of patients after cardiac surgery and requires dialysis in 1% of cases and associated with an increased risk of mortality and morbidity, predisposes patients to a longer hospitalization, requires additional treatments, and increases the hospital costs. We aimed to investigate the factors affecting the progression of kidney disease during cardiac surgery in preoperative chronic kidney disease patients (CKD).
Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis

Abstract Ultraviolet (UV) induces pyrimidine dimers (PDs) in DNA and replication-dependent fragmentation in chromosomes. The rnhAB mutants in Escherichia coli, accumulating R-loops and single DNA-rNs, are generally resistant to DNA damage, but are surprisingly UV-sensitive, even though they remove PDs normally, suggesting irreparable chromosome lesions. We show here that the RNase H defect does not cause additional chromosome fragmentation after UV, but inhibits DNA synthesis after replication restart. Genetic analysis implies formation of R-loop-anchored transcription elongation complexes (R-loop-aTECs) in UV-irradiated rnhAB mutants, predicting that their chromosomal DNA will accumulate: (i) RNA:DNA hybrids; (ii) a few slow-to-remove PDs. We confirm both features and also find that both, surprisingly, depend on replication restart. Finally, enriching for the UV-induced RNA:DNA hybrids in the rnhAB uvrA mutants also co-enriches for PDs, showing their co-residence in the same structures. We propose that PD-triggered R-loop-aTECs block head-on replication in RNase H-deficient mutants.
Fall-related events in people who are lower limb prosthesis users: the lived experience

Abstract Purpose To explore lived experiences, and identify common themes as well as vocabulary associated with fall-related events in lower limb prosthesis (LLP) users. Materials and methods Five focus groups of LLP users from across the United States were conducted remotely via video or tele-conferencing. Focus group transcripts were coded and analyzed using methods adapted from a grounded theory approach to identify themes. Results Focus group participants (n = 25) described experiences associated with fall-related events that resulted in the identification of six themes: (1) memories of fall-related events are shaped by time and context, (2) location and ground conditions influence whether falls occur, (3) some activities come with more risk, (4) fall-related situations are multi-faceted, and often involve the prosthesis, (5) how LLP users land, but not the way they go down, tends to vary, and (6) not all falls affect LLP users, but some near-falls do. Conclusion Consideration for where LLP users fall, what they are doing when they fall, how they fall, what occurs as a result of a fall, and how well memory of a fall persists may enhance recording and reporting of falls, contribute to development of improved fall risk assessment tools, and inspire the design and function of prosthetic componentry for patient safety. Implications for rehabilitation Falls are a common problem in lower limb prosthesis (LLP) users that can lead to adverse health outcomes. Concerns over near falls, not just falls, may merit greater attention from rehabilitation professionals. Elements of the lived experience that appear unique to LLP users include the role of prosthetic fit, function, and comfort in losing and/or recovering balance; as well as the tendency of LLP users to modify rather than stop or avoid activities associated with falls.
Association of premature menopause with incident pulmonary hypertension: A cohort study

Background Several forms of pulmonary hypertension (PH) disproportionately affect women. Animal and human studies suggest that estradiol exerts mixed effects on the pulmonary vasculature. Whether premature menopause represents a risk factor for PH is unknown. Methods and findings In this cohort study, women in the UK Biobank aged 40–69 years who were postmenopausal and had complete data available on reproductive history were included. Premature menopause, defined as menopause occurring before age 40 years. Postmenopausal women without premature menopause served as the reference group. The primary outcome was incident PH, ascertained by appearance of a qualifying ICD code in the participant’s UK Biobank study record. Of 136,715 postmenopausal women included, 5,201 (3.8%) had premature menopause. Participants were followed up for a median of 11.1 (interquartile range 10.5–11.8) years. The primary outcome occurred in 38 women (0.73%) with premature menopause and 409 (0.31%) without. After adjustment for age, race, ever-smoking, body-mass index, systolic blood pressure, antihypertensive medication use, non-high-density lipoprotein cholesterol, cholesterol-lowering medication use, C-reactive protein, prevalent type 2 diabetes, obstructive sleep apnea, heart failure, mitral regurgitation, aortic stenosis, venous thromboembolism, forced vital capacity (FVC), the forced expiratory volume in 1 second-to-FVC ratio, use of menopausal hormone therapy, and hysterectomy status, premature menopause was independently associated with PH (hazard ratio 2.13, 95% CI 1.31–3.23, P<0.001). In analyses of alternate menopausal age thresholds, risk of PH appeared to increase progressively with younger age at menopause (Ptrend <0.001), with 4.8-fold risk in women with menopause before age 30 years (95% CI 1.82–12.74, P = 0.002). Use of menopausal hormone therapy did not modify the association of premature menopause with PH. Conclusions Premature menopause may represent an independent risk factor for PH in women. Further investigation of the role of sex hormones in PH is needed in animal and human studies to elucidate pathobiology and identify novel therapeutic targets.
Bilateral Acanthamoeba keratitis with radial keratoneuritis – utility of AS-OCT in management and treatment

Acanthamoeba keratitis (AK) is a rare but vision-threatening keratitis that is usually unilateral; however, it has been reported to be bilateral with the use of contact lenses or orthokeratology. Apart from contact lens use, in developing countries, AK is also associated with trauma to the eye, exposure to contaminated soil or water, warmer climates, and poor socio-economic conditions. AK can present as patchy stromal infiltrates, stromal ring infiltrate, epithelial haze, and radial keratoneuritis. Early presentation is usually non-specific and can be misdiagnosed as herpetic keratitis in almost 75–90% of cases due to the presence of pseudodendrites. Although considered pathognomic of AK, radial keratoneuritis can also be present in Pseudomonas or viral keratitis; therefore, early presentation in contact lens users is usually confused with these conditions. Radial keratoneuritis in AK represents the inflamed nerves surrounded by trophozoites. Although microbiology can help derive a definitive diagnosis by isolating the cysts or trophozoites of Acanthamoeba, noninvasive in vivo confocal microscopy and anterior-segment optical coherence tomography (AS-OCT) can be used as an adjunct for diagnosis of AK. This approach can serve as a modality to monitor the resolution of the disease and determine the appropriate time for stopping the antiacanthamoebal therapy. AS-OCT is a non-contact low-coherence interferometry imaging, which provides a high-resolution cross-sectional image of the eye (4-7microns). Traditionally, AS-OCT is used in deriving quantitative measures of corneal thickness, assessing anterior chamber angle architecture, identifying corneal ectasias, iris and lenticular abnormalities, and detecting intraocular masses. Recently it has also been used to objectively demonstrate radial keratoneuritis that appears as highly reflective radial bands or lines at stromal level. The advantage of using AS-OCT over slitlamp biomicroscopy is that it not only objectively documents corneal changes but also provides a precise measure of corneal thickness, allowing better monitoring of disease progression and treatment response. Secondly, the reflectivity serves as a marker for disease activity and change in intensity can indirectly help in assessing the density of cellular material causing inflammation. This report documents a case of microbiologically proven contact lens-related bilateral AK with radial keratoneuritis in which AS-OCT was used to objectively visualise the radial keratoneuritis and monitor treatment course.
Improving colour extraction and stability in red wines: the use of maceration enzymes and enological tannins

Summary Two commercially available maceration enzymes and two enological tannins were tested in Monastrell wines to determine their suitability for improving the chromatic characteristics, colour stability and sensory properties of the resulting wines. The greatest differences for all the wines, when comparing with the control wine, were observed at the beginning of the winemaking process, any differences diminishing in the finished wines. One of the enzyme-treated wines was used showed hardly any difference from the control wine, whereas the other enzyme-treated wine showed an improvement in their chromatic and sensory characteristics. The use of two different enological tannins did not provide any improvement in the chromatic and sensory characteristics of the wines, imparting a higher yellow colour and resulting in lower scores in the colour and aroma sensory characteristics, accompanied by a higher astringency, dryness and bitter sensory sensations.