Miracle-dz/UniFAR-FTUs huggingface dataset:
Network-based Transcript Quantification with RNA-Seq Data

High-throughput mRNA sequencing (RNA-Seq) provides valuable information for accurate transcript quantification. In this paper, we introduce a Networkbased method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction information with short read alignment for transcript abundance estimation. Based on the observation that the abundances of the neighboring transcripts by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with a heuristic alternating optimization algorithm. We demonstrate in the experiments that (1) qRT-PCR confirmed that Net-RSTQ achieves better transcript quantification accuracy with RNA-Seq data from a stem cell line and an ovarian cancer cell line compared with the models without using transcript network; and (2) the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification tested on the RNA-Seq data of ovarian cancer, breast cancer and lung cancer in The Cancer Genome Atlas (TCGA).
Clinical, FDG-PET and molecular markers of immune checkpoint inhibitor response in patients with metastatic Merkel cell carcinoma

Background Metastatic Merkel cell carcinoma (mMCC) is an aggressive neuroendocrine malignancy of the skin with a poor prognosis. Immune checkpoint inhibitors (ICIs) have shown substantial efficacy and favorable safety in clinical trials. Methods Medical records of patients (pts) with mMCC treated with ICIs from August 2015 to December 2018 at Peter MacCallum Cancer Centre in Australia were analyzed. Response was assessed with serial imaging, the majority with FDG-PET/CT scans. RNA sequencing and immunohistochemistry for PD-L1, CD3 and Merkel cell polyomavirus (MCPyV) on tumor samples was performed. Results 23 pts with mMCC were treated with ICIs. A median of 8 cycles (range 1 to 47) were administered, with treatment ongoing in 6 pts. Objective responses (OR) were observed in 14 pts (61%): 10 (44%) complete responses (CR) and 4 (17%) partial responses (PR). Median time to response was 8 weeks (range 6 to 12) and 12-month progression-free survival rate was 39%. Increased OR were seen in pts aged less than 75 (OR 80% vs 46%), no prior history of chemotherapy (OR 64% vs 50%), patients with an immune-related adverse event (OR 100% vs 43%) and in MCPyV-negative tumors (OR 69% vs 43%). Pts with a CR had lower mean metabolic tumor volume on baseline FDG-PET/CT scan (CR: 35.7 mL, no CR: 187.8 mL, p=0.05). There was no correlation between PD-L1 positivity and MCPyV status (p=0.764) or OR (p=0.245). 10 pts received radiation therapy (RT) during ICI: 4 pts started RT concurrently (OR 75%, CR 50%), 3 pts had isolated ICI-resistant lesions successfully treated with RT and 3 pts with multisite progression continued to progress despite RT. Overall, 6 pts (26%) had grade 1–2 immune-related adverse events. Conclusion ICIs showed efficacy and safety in mMCC consistent with trial data. Clinical and imaging predictors of response were identified.
Passivity and Dissipativity of Fractional-Order Quaternion-Valued Fuzzy Memristive Neural Networks: Nonlinear Scalarization Approach

In this article, the problem of passivity and dissipativity analysis is investigated for a class of fractional-order quaternion-valued fuzzy memristive neural networks. Based on the famous nonlinear scalarizing function, a nonlinear scalarization method is developed, which can be employed to compare the “size” of two different quaternions. In this way, the convex closure proposed by the quaternion-valued connection weights is meaningful. By constructing proper Lyapunov functional, several improved passivity criteria and dissipativity conclusions are established, which can be checked efficiently by utilizing some standard mathematical calculations. Finally, the obtained results are validated by simulation examples.
Molecular taxonomy and community dynamics of Actinobacteria in marine sediments off central Chile

Se uso pirosecuenciacion de la region V6 del gen 16S del ARNr para caracterizar la diversidad y la dinamica espacio-temporal de unidades taxonomicas operacionales (OTUs) del filo Actinobacteria, los que fueron aislados desde sedimentos provenientes del Sulfureto de Humboldt frente a Chile central. Este substrato es rico en compuestos azufrados y material organico lo que mantiene una vasta comunidad microbiana que experimenta cambios estacionales en respuesta a regimenes oceanograficos contrastantes. Se identificaron 498 OTUs distribuidas en 7 ordenes, 47 familias, 122 generos, (5 de los cuales son ampliamente reconocidos por sus aplicaciones biotecnologicas), y 56 especies. El analisis temporal revelo que algunos OTUs presentan diferencias significativas en abundancia, indices de diversidad y riqueza, las que generaron una agrupacion de las muestras asociada a la fecha de muestreo (estacion del ano) y no a la profundidad del sitio de muestreo. Debido a que las Actinobacteria son mayormente aerobicas, las altas concentraciones de oxigeno disuelto que ocurren en la zona en el otono-invierno austral, representan condiciones ambientales beneficiosas para este filo, no asi las de primavera-verano austral cuando prevalece la hipoxia. El presente trabajo se beneficio de la aplicacion de metodos cultivo-independientes (metodos moleculares) para evaluar la diversidad taxonomica y examinar la dinamica de uno de los grupos de bacterias presentes en el Sulfureto de Humboldt reportado como una fuente potencial e inexplorada de metabolitos secundarios.
Biological fixation of CO2 by Chlorella sp HA-1 in a semi-continuous and series reactor system

Characteristics of biological CO 2 fixation by Chlorella sp. HA-1 were investigated in a semi-continuous and series reactor system using an internally illuminated photobioreactor to overcome shortcomings of physicochemical technologies such as adsorption and membrane separation. High CO 2 fixation rate was achieved in the semi-continuous reactor system, in which the dilution ratios of the culture medium were controlled. The average CO 2 fixation rate was maintained almost constantly when the dilution ratio increased by 0.1 increment from the initial value of 0.5. The total removal efficiency of CO 2 was enhanced by employing a series reactor system. The average CO 2 fixation rate increased until 4.013 g CO 2 day -1 in a series operation of four reactors, compared to 0.986 g CO 2 day -1 in a batch operation mode. The total CO 2 fixation rate was proportional to the number of reactors used in the series reactor system. In the series reactor system of semi-continuous operation, a large amount of CO 2 was removed continuously for 30 days. These results showed that the present reactor systems are efficient and economically feasible for a biological CO 2 fixation.
Distinct influence of parental occupation on cortical thickness and surface area in children and adolescents: Relation to self‐esteem

Studies of socioeconomic disparities have largely focused on correlating brain measures with either composite measure of socioeconomic status (SES), or its components—family income or parental education, giving little attention to the component of parental occupation. Emerging evidence suggests that parental occupation may be an important and neglected indicator of childhood and adolescent SES compared to absolute measures of material resources or academic attainment because, while related, it may more precisely capture position in social hierarchy and related health outcomes. On the other hand, although cortical thickness and surface area are brain measures with distinct genetic and developmental origins, large‐scale neuroimaging studies investigating regional differences in interaction of the composite measure of SES or its components with cortical thickness and surface area are missing. We set out to fill this gap, focusing specifically on the role of parental occupation on cortical thickness and surface area by analyzing magnetic resonance imaging scans from 704 healthy individuals (age = 3–21 years). We observed spatially distributed patterns of (parental occupation × age2) interaction with cortical thickness (localized at the left caudal middle frontal, the left inferior parietal and the right superior parietal) and surface area (localized at the left orbitofrontal cortex), indicating independent sources of variability. Further, with decreased cortical thickness, children from families with lower parental occupation exhibited lower self‐esteem. Our findings demonstrate distinct influence of parental occupation on cortical thickness and surface area in children and adolescents, potentially reflecting different neurobiological mechanisms by which parental occupation may impact brain development.
Using a patient-reported outcome to improve detection of cognitive impairment and dementia: The patient version of the Quick Dementia Rating System (QDRS)

Introduction Community detection of mild cognitive impairment (MCI) and Alzheimer’s disease and related disorders (ADRD) is a challenge. While Gold Standard assessments are commonly used in research centers, these methods are time consuming, require extensive training, and are not practical in most clinical settings or in community-based research projects. Many of these methods require an informant (e.g., spouse, adult child) to provide ratings of the patients’ cognitive and functional abilities. A patient-reported outcome that captures the presence of cognitive impairment and corresponds to Gold Standard assessments could improve case ascertainment, clinical care, and recruitment into clinical research. We tested the patient version of the Quick Dementia Rating System (QDRS) as a patient-reported outcome to detect MCI and ADRD. Methods The patient QDRS was validated in a sample of 261 consecutive patient-caregiver dyads compared with the informant version of the QDRS, the Clinical Dementia Rating (CDR), neuropsychological tests, and Gold Standard measures of function, behavior, and mood. Psychometric properties including item variability, floor and ceiling effects, construct, concurrent, and known-groups validity, and internal consistency were determined. Results The patient QDRS strongly correlated with Gold Standard measures of cognition, function, mood, behavior, and global staging methods (p-values < .001) and had strong psychometric properties with excellent data quality and internal consistency (Cronbach alpha = 0.923, 95%CI:0.91–0.94). The patient QDRS had excellent agreement with the informant QDRS, the CDR and its sum of boxes (Intraclass Correlation Coefficients: 9.781–0.876). Receiver operator characteristic curves showed excellent discrimination between normal controls from CDR 0.5 (AUC:0.820;95% CI: 0.74–0.90) and for normal controls from any cognitive impairment (AUC:0.885;95% CI: 0.83–0.94). Discussion The patient QDRS validly and reliably differentiates individuals with and without cognitive impairment and can be completed by patients through all stages of dementia. The patient QDRS is highly correlated with Gold Standard measures of cognitive, function, behavior, and global staging. The patient QDRS provides a rapid method to screen patients for MCI and ADRD in clinical practice, determine study eligibility, improve case ascertainment in community studies.
Phosphorus Bioavailability: A Key Aspect for Conserving this Critical Animal Feed Resource with Reference to Broiler Nutrition

Phosphorus (P) is an essential element, and the majority of animal feed phosphate is derived from phosphate rock that is a non-renewable resource. Current global P reserves may be depleted in 50–100 years. This poses the challenge of securing future P supply for the global animal feed industries. Currently, nutritionists formulate diets with substantial safety margins to guarantee that animals do not become P deficient. Excessive dietary P concentrations increase, not only the cost of diets, but also P excretion and pollution of the environment. We contend that understanding P bioavailability is central to the sustainable use of this mineral in animal agriculture. Poultry accounts for approximately 50% of animal feed phosphate consumption worldwide and for this reason we use the meat chicken or broiler as a case study to explore the nuances of P bioavailability. We conclude that, to tackle the challenge of dietary P bioavailability, cooperative research on a global scale is needed to standardise measurement procedures in order to produce a robust and reliable database which can be used by nutritionists to formulate diets to meet the bird’s P requirements precisely. Achievement of this goal will assist endeavours to sustain the global supply of phosphorus.
A correction to a recent review of the genus Hemidactylus Goldfuss, 1820 (Squamata: Gekkonidae) from Angola, with the description of two additional species.

A correction to the recent revision of the genus Hemidactylus Goldfuss, 1820 from Angola is presented. The previous revision assigned some historical specimens to H. bayonii and H. nzingae, with one specimen even being considered a paratype of the latter taxon. A review of the morphological data of all of the specimens used in the previous study found that two other undescribed taxa, morphologically similar to H. bayonii and H. nzingae, respectively, were overlooked. We here present a re-description of these specimens and provide the diagnostic characters that allow their recognition as two new species, both endemic to Angola. In order to provide an accurate picture of the diversity of Hemidactylus in the country and to correct our previous misidentifications that could lead to some taxonomic instability, we herein describe H. hannasabinae sp. nov. and H. vernayi sp. nov.
Monocloning oligoclonality - dissecting the humoral immune response in central nervous system inflammations

Neuroborreliosis (NB) is a chronic infectious disease of the central nervous system caused by a tick borne spirochete, Borrelia burgdorferi (Bb). In addition to direct effects of the causative infectious agent, additional immune mediated mechanisms are thought to play a role in the central nervous system (CNS) pathology of NB. In order to further understand the involvement of humoral immune mechanisms in NB, we dissected the intrathecal antibody responses down to the single plasma cell level. Starting with single cell RT-PCR of FACS sorted cerebrospinal fluid plasma cells from a NB patient, we identified expanded clones and resurrected the antigen specificity of their secreted antibodies through recombinant expression of the correctly paired Ig heavy and light chain genes as monoclonal antibodies (mAb). As expected, we found specificity for the causative infectious agent Bb among the clonally expanded plasma cell (cePC) derived mAb. However, from an independent cePC of the same patient, we could derive mAbs specific for human CNS myelin, without detectable crossreactivity with Bb antigens. While reactivity against Bb is a known feature of humoral immune responses in NB, we show a) that immune responses specific for self-antigens may be a distinct feature of CNS infections independent of pathogen reactivity and b) that humoral autoimmunity in NB – since found in cePC is the result of a truly antigen driven immune response. Our findings indicate that in NB mechanisms may be at play that induce distinct immune responses specific for pathogen and self-antigens independent from “molecular mimicry”. Original Research Articles 35 Thesis author work: This manuscript is the thesis core and experiments were mainly performed by myself. Contributions from other people comprise part of the immunofluorescence experiments and help in preparing the manuscript. Original Research Articles 36 Clonally expanded plasma cells in the CSF of MS patients produce CNS specific immunoglobulins Hans-Christian von Büdingen, Melanie D. Harrer, Sandra Kuenzle, Mirjam Meier, Tobias A. Rupprecht and Norbert Goebels # HCVB, MH and SK contributed equally
Spin reorientation in antiferromagnetic Dy2FeCoO6 double perovskite

We explored the electronic and magnetic properties of the lanthanide double perovskite Dy2FeCoO6 by combining magnetization, Raman and Mössbauer spectroscopy and neutron diffraction along with density functional theory (DFT) calculations. Our magnetization measurements revealed two magnetic phase transitions in Dy2FeCoO6. First, a paramagnetic to antiferromagnetic transition at T N = 248 K and subsequently, a spin reorientation transition at T SR = 86 K. In addition, a field-induced magnetic phase transition with a critical field of H c ≈ 20 kOe is seen at 2 K. Neutron diffraction data suggested cation-disordered orthorhombic structure for Dy2FeCoO6 in Pnma space group which is supported by Raman scattering results. The magnetic structures ascertained through representational analysis indicate that at T N, a paramagnetic state is transformed to Γ5(Cx, Fy, Az) antiferromagnetic structure while, at T SR, Fe/Co moments undergo a spin reorientation to Γ3(Gx, Ay, Fz). The refined magnetic moment of (Fe/Co) is 1.47(4) μ B at 7 K. The antiferromagnetic structure found experimentally is supported through the DFT calculations which predict an insulating electronic state in Dy2FeCoO6.
Comparing recombinant MPB70/SahH and native 20-kDa protein for detecting bovine tuberculosis using ELISA

Bovine tuberculosis (bTB) is a zoonosis caused by Mycobacterium bovis. Test-and-cull protocols and gross pathological examinations of abattoir animals as well as milk pasteurization have been implemented to prevent the spread of tuberculosis from animals to humans worldwide. Despite the importance of precise and rapid diagnostic tests, conventional methods including intradermal skin tests and γ-interferon assays are limited by the high rate of false-negative results for cattle in the late infectious stage and due to laborious and time-consuming procedures. Therefore, antibody detection methods such as enzyme-linked immunosorbent assay (ELISA) are urgently needed to supplement the established approaches and expand the diagnostic window. This study was conducted to develop a bTB ELISA by evaluating recombinant and native proteins and various assay parameters. We produced recombinant MPB70 and SahH (M70S) and a native 20-kDa protein (20K) and optimized the ELISA protocol. The 20K ELISA showed 94.4% sensitivity and 98.2% specificity with an optimal sample-to-positive ratio cut-off of 0.531. The sensitivity and specificity of M70S ELISA were 94.4% and 97.3%, respectively, with an optimal sample-to-negative ratio cut-off of 1.696. Both assays showed acceptable diagnostic efficiency and could be used for bTB diagnosis in combination with established methods for herd screening and to expand the diagnostic window.
Investigation of the Effect of Channel Structure and Flow Rate on On-Chip Bacterial Lysis

Successful lysis of cells/microorganisms is a key step in the sample preparation in fields like molecular biology, bioengineering, and biomedical engineering. This study therefore aims to investigate the lysis of bacteria on-chip and its dependence on both microfluidic channel structure and flow rate. Effects of temperature on lysis on-chip were also investigated. To perform these investigations, three different microfluidic chips were designed and produced (straight, zigzag and circular configurations), while the length of the channels were kept constant. As an exemplary case, Mycobacterium smegmatis was chosen to represent the acid-fast bacteria. Bacterial suspensions of 1.5 McFarland were injected into the chips at various flow rates (0.6- $8~\mu \text{l}$ /min) either at room temperature or 50° C. In order to understand the on-chip lysis performance fully, off-chip experiments were carried out at durations which are equal to those bacteria spent in the channel from inlet to the outlet at different flow rates. We also performed COMSOL multiphysics program simulations to evaluate further the effect of the applied parameters. As a result, we found that the structure and the flow rate do not affect lysis over all in all investigated channel types, however on-chip experiments at room temperature produced more effective lysis compared to the on-chip and the off-chip samples performed at higher temperatures. Interestingly on-chip experiments at higher tempratures do not result in effective lysis.
An investigation of in-ear sensing for motor task classification

Objective. Our study aims to investigate the feasibility of in-ear sensing for human–computer interface. Approach. We first measured the agreement between in-ear biopotential and scalp-electroencephalogram (EEG) signals by channel correlation and power spectral density analysis. Then we applied EEG compact network (EEGNet) for the classification of a two-class motor task using in-ear electrophysiological signals. Main results. The best performance using in-ear biopotential with global reference reached an average accuracy of 70.22% (cf 92.61% accuracy using scalp-EEG signals), but the performance in-ear biopotential with near-ear reference was poor. Significance. Our results suggest in-ear sensing would be a viable human–computer interface for movement prediction, but careful consideration should be given to the position of the reference electrode.
Survival and infestivity of Sarcoptes scabiei vat. canis and vat. hominis

Sarcoptes scabiei vat. canis served as a suitable model for the study of S. scabiei var. hominis survival. S. scabiei var. canis and vat. hominis mites were found to survive off the host for 24 to 36 hours at room conditions (21 ° C and 40% to 80% relative humidity [RH]), and the canine variety survived I9 days at 10 ° C and 97% RH. Female mites survived decidedly longer than male mites at comparable conditions. Generally, higher RH values and lower temperatures favored survival, whereas higher temperature and lower RH led to early death. Most canine scabies mites that were held off the host for 36 hours at 75% RH and 22 ° to 24" C remained infestive and penetrated when returned to the host. Live mites of the human variety that were recovered from bed linen slept on by infested patients would also penetrate a host after being held off a host for 96 hours in alternating 12-hour periods of room conditions and refrigeration. Penetration required less than 30 minutes for all life stages of both varieties, and it was accomplished by a mite secretion that dissolved the host tissue. Dislodged mites, particularly those in close