Miracle-dz/UniFAR-FTUs huggingface dataset:
Missing-value estimation using linear and non-linear regression with Bayesian gene selection

MOTIVATION Data from microarray experiments are usually in the form of large matrices of expression levels of genes under different experimental conditions. Owing to various reasons, there are frequently missing values. Estimating these missing values is important because they affect downstream analysis, such as clustering, classification and network design. Several methods of missing-value estimation are in use. The problem has two parts: (1) selection of genes for estimation and (2) design of an estimation rule. RESULTS We propose Bayesian variable selection to obtain genes to be used for estimation, and employ both linear and nonlinear regression for the estimation rule itself. Fast implementation issues for these methods are discussed, including the use of QR decomposition for parameter estimation. The proposed methods are tested on data sets arising from hereditary breast cancer and small round blue-cell tumors. The results compare very favorably with currently used methods based on the normalized root-mean-square error. AVAILABILITY The appendix is available from http://gspsnap.tamu. edu/gspweb/zxb/missing_zxb/ (user: gspweb; passwd: gsplab).
Domain walls in strontium titanate

Density functional theory calculations of twin-domain walls in strontium titanate are presented. The two possible domain walls are characterized. The domain wall type is set by the relative phase of the octahedral rotations in the body-centered-tetragonal SrTiO$_3$ on either side of the domain wall. The width of the domain walls is estimated to be approximately 3 nm.
Effects of Enzyme Replacement Therapy Started Late in a Murine Model of Mucopolysaccharidosis Type I

Mucopolysaccharidosis type I (MPS I) is a progressive disorder caused by deficiency of α-L-iduronidase (IDUA), which leads to storage of heparan and dermatan sulphate. It is suggested that early enzyme replacement therapy (ERT) leads to better outcomes, although many patients are diagnosed late and don’t receive immediate treatment. This study aims to evaluate the effects of late onset ERT in a MPS I murine model. MPS I mice received treatment from 6 to 8 months of age (ERT 6–8mo) with 1.2mg laronidase/kg every 2 weeks and were compared to 8 months-old wild-type (Normal) and untreated animals (MPS I). ERT was effective in reducing urinary and visceral GAG to normal levels. Heart GAG levels and left ventricular (LV) shortening fraction were normalized but cardiac function was not completely improved. While no significant improvements were found on aortic wall width, treatment was able to significantly reduce heart valves thickening. High variability was found in behavior tests, with treated animals presenting intermediate results between normal and affected mice, without correlation with cerebral cortex GAG levels. Cathepsin D activity in cerebral cortex also did not correlate with behavior heterogeneity. All treated animals developed anti-laronidase antibodies but no correlation was found with any parameters analyzed. However, intermediary results from locomotion parameters analyzed are in accordance with intermediary levels of heart function, cathepsin D, activated glia and reduction of TNF-α expression in the cerebral cortex. In conclusion, even if started late, ERT can have beneficial effects on many aspects of the disease and should be considered whenever possible.
Enhancing Digital Fabrication with Advanced Modeling Techniques

A few years ago there were only expensive machineries dedicated to rapid prototyping for professionals or industrial application, while nowadays very aﬀordable solutions are on the market and have become useful tools for experimenting, providing access to ﬁnal users. Given the digital nature of these machine-controlled manufacturing processes, a clear need exists for computational tools that support this new way of productional thinking. For this reason the ultimate target of this research is to improve the easiness of use of such technologies, providing novel supporting tools and methods to ultimately sustain the concept of democratized design (“fabrication for the masses”). In this thesis we present a novel set of methods to enable, with the available manufacturing devices, new cost-eﬀective and powerful ways of producing objects. The contributions of the thesis are three. The ﬁrst one is a technique that allows to automatically create a tangible illustrative representation of a 3D model by interlocking together a set of planar pieces, which can be fabricated using a 2D laser cutter. The second method allows to automatically design ﬂexible reusable molds to produce many copies of an input digital object. The designs produced by this method can be directly sent to a 3D printer and used to liquid-cast multiple replicas using a wide variety of materials. The last technique is a method to fabricate, using a single-material 3D printer, objects with custom elasticity, and an optimization strategy that, varying the elastic properties inside the volume, is able to design printable objects with a prescribed mechanical behavior.
Host Phenology and Geography as Drivers of Differentiation in Generalist Fungal Mycoparasites

The question as to why parasites remain generalist or become specialist is a key unresolved question in evolutionary biology. Ampelomyces spp. , intracellular mycoparasites of powdery mildew fungi, which are themselves plant pathogens, are a useful model for studies of this issue. Ampelomyces is used for the biological control of mildew. Differences in mycohost phenology promote temporal isolation between sympatric Ampelomyces mycoparasites. Apple powdery mildew (APM) causes spring epidemics, whereas other powdery mildew species on plants other than apple cause epidemics later in the season. This has resulted in genetic differentiation between APM and non-APM strains. It is unclear whether there is genetic differentiation between non-APM Ampelomyces lineages due to their specialization on different mycohosts. We used microsatellites to address this question and found no significant differentiation between non-APM Ampelomyces strains from different mycohosts or host plants, but strong differentiation between APM and non-APM strains. A geographical structure was revealed in both groups, with differences between European countries, demonstrating restricted dispersal at the continent scale and a high resolution for our markers. We found footprints of recombination in both groups, possibly more frequent in the APM cluster. Overall, Ampelomyces thus appears to be one of the rare genuine generalist pathogenic fungi able to parasitize multiple hosts in natural populations. It is therefore an excellent model for studying the evolution of pathogens towards a generalist rather than host-specific strategy, particularly in light of the tritrophic interaction between Ampelomyces mycoparasites, their powdery mildew fungal hosts and the mildew host plants.
Using Massive Parallel Sequencing for the Development, Validation, and Application of Population Genetics Markers in the Invasive Bivalve Zebra Mussel (Dreissena polymorpha)

The zebra mussel (Dreissena polymorpha, Pallas, 1771) is one of the most invasive species of freshwater bivalves, due to a combination of biological and anthropogenic factors. Once this species has been introduced to a new area, individuals form dense aggregations that are very difficult to remove, leading to many adverse socioeconomic and ecological consequences. In this study, we identified, tested, and validated a new set of polymorphic microsatellite loci (also known as SSRs, Single Sequence Repeats) using a Massive Parallel Sequencing (MPS) platform. After several pruning steps, 93 SSRs could potentially be amplified. Out of these SSRs, 14 were polymorphic, producing a polymorphic yield of 15.05%. These 14 polymorphic microsatellites were fully validated in a first approximation of the genetic population structure of D. polymorpha in the Iberian Peninsula. Based on this polymorphic yield, we propose a criterion for establishing the number of SSRs that require validation in similar species, depending on the final use of the markers. These results could be used to optimize MPS approaches in the development of microsatellites as genetic markers, which would reduce the cost of this process.
Dental Ontogeny in Pliocene and Early Pleistocene Hominins

Until recently, our understanding of the evolution of human growth and development derived from studies of fossil juveniles that employed extant populations for both age determination and comparison. This circular approach has led to considerable debate about the human-like and ape-like affinities of fossil hominins. Teeth are invaluable for understanding maturation as age at death can be directly assessed from dental microstructure, and dental development has been shown to correlate with life history across primates broadly. We employ non-destructive synchrotron imaging to characterize incremental development, molar emergence, and age at death in more than 20 Australopithecus anamensis, Australopithecus africanus, Paranthropus robustus and South African early Homo juveniles. Long-period line periodicities range from at least 6–12 days (possibly 5–13 days), and do not support the hypothesis that australopiths have lower mean values than extant or fossil Homo. Crown formation times of australopith and early Homo postcanine teeth fall below or at the low end of extant human values; Paranthropus robustus dentitions have the shortest formation times. Pliocene and early Pleistocene hominins show remarkable variation, and previous reports of age at death that employ a narrow range of estimated long-period line periodicities, cuspal enamel thicknesses, or initiation ages are likely to be in error. New chronological ages for SK 62 and StW 151 are several months younger than previous histological estimates, while Sts 24 is more than one year older. Extant human standards overestimate age at death in hominins predating Homo sapiens, and should not be applied to other fossil taxa. We urge caution when inferring life history as aspects of dental development in Pliocene and early Pleistocene fossils are distinct from modern humans and African apes, and recent work has challenged the predictive power of primate-wide associations between hominoid first molar emergence and certain life history variables.
Quantifying the Shape of Aging

In Biodemography, aging is typically measured and compared based on aging rates. We argue that this approach may be misleading, because it confounds the time aspect with the mere change aspect of aging. To disentangle these aspects, here we utilize a time-standardized framework and, instead of aging rates, suggest the shape of aging as a novel and valuable alternative concept for comparative aging research. The concept of shape captures the direction and degree of change in the force of mortality over age, which—on a demographic level—reflects aging. We 1) provide a list of shape properties that are desirable from a theoretical perspective, 2) suggest several demographically meaningful and non-parametric candidate measures to quantify shape, and 3) evaluate performance of these measures based on the list of properties as well as based on an illustrative analysis of a simple dataset. The shape measures suggested here aim to provide a general means to classify aging patterns independent of any particular mortality model and independent of any species-specific time-scale. Thereby they support systematic comparative aging research across different species or between populations of the same species under different conditions and constitute an extension of the toolbox available to comparative research in Biodemography.
Single-cell analyses reveal an attenuated NF-κB response in the Salmonella-infected fibroblast

ABSTRACT The eukaryotic transcriptional regulator Nuclear Factor kappa B (NF-κB) plays a central role in the defense to pathogens. Despite this, few studies have analyzed NF-κB activity in single cells during infection. Here, we investigated at the single cell level how NF-κB nuclear localization – a proxy for NF-κB activity – oscillates in infected and uninfected fibroblasts co-existing in cultures exposed to Salmonella enterica serovar Typhimurium. Fibroblasts were used due to the capacity of S. Typhimurium to persist in this cell type. Real-time dynamics of NF-κB was examined in microfluidics, which prevents cytokine accumulation. In this condition, infected (ST+) cells translocate NF-κB to the nucleus at higher rate than the uninfected (ST-) cells. Surprisingly, in non-flow (static) culture conditions, ST- fibroblasts exhibited higher NF-κB nuclear translocation than the ST+ population, with these latter cells turning refractory to external stimuli such as TNF-α or a second infection. Sorting of ST+ and ST- cell populations confirmed enhanced expression of NF-κB target genes such as IL1B, NFKBIA, TNFAIP3, and TRAF1 in uninfected (ST-) fibroblasts. These observations proved that S. Typhimurium dampens the NF-κB response in the infected fibroblast. Higher expression of SOCS3, encoding a “suppressor of cytokine signaling,” was also observed in the ST+ population. Intracellular S. Typhimurium subverts NF-κB activity using protein effectors translocated by the secretion systems encoded by pathogenicity islands 1 (T1) and 2 (T2). T1 is required for regulating expression of SOCS3 and all NF-κB target genes analyzed whereas T2 displayed no role in the control of SOCS3 and IL1B expression. Collectively, these data demonstrate that S. Typhimurium attenuates NF-κB signaling in fibroblasts, an effect only perceptible when ST+ and ST- populations are analyzed separately. This tune-down in a central host defense might be instrumental for S. Typhimurium to establish intracellular persistent infections.
Multiple Requirements of PLK1 during Mouse Oocyte Maturation

Polo-like kinase 1 (PLK1) orchestrates multiple events of cell division. Although PLK1 function has been intensively studied in centriole-containing and rapidly cycling somatic cells, much less is known about its function in the meiotic divisions of mammalian oocytes, which arrest for a long period of time in prophase before meiotic resumption and lack centrioles for spindle assembly. Here, using specific small molecule inhibition combined with live mouse oocyte imaging, we comprehensively characterize meiotic PLK1’s functions. We show that PLK1 becomes activated at meiotic resumption on microtubule organizing centers (MTOCs) and later at kinetochores. PLK1 is required for efficient meiotic resumption by promoting nuclear envelope breakdown. PLK1 is also needed to recruit centrosomal proteins to acentriolar MTOCs to promote normal spindle formation, as well as for stable kinetochore-microtubule attachment. Consequently, PLK1 inhibition leads to metaphase I arrest with misaligned chromosomes activating the spindle assembly checkpoint (SAC). Unlike in mitosis, the metaphase I arrest is not bypassed by the inactivation of the SAC. We show that PLK1 is required for the full activation of the anaphase promoting complex/cyclosome (APC/C) by promoting the degradation of the APC/C inhibitor EMI1 and is therefore essential for entry into anaphase I. Moreover, our data suggest that PLK1 is required for proper chromosome segregation and the maintenance of chromosome condensation during the meiosis I-II transition, independently of the APC/C. Thus, our results define the meiotic roles of PLK1 in oocytes and reveal interesting differential requirements of PLK1 between mitosis and oocyte meiosis in mammals.
Plasmodium vivax and Plasmodium falciparum at the Crossroads of Exchange among Islands in Vanuatu: Implications for Malaria Elimination Strategies

Understanding the transmission and movement of Plasmodium parasites is crucial for malaria elimination and prevention of resurgence. Located at the limit of malaria transmission in the Pacific, Vanuatu is an ideal candidate for elimination programs due to low endemicity and the isolated nature of its island setting. We analyzed the variation in the merozoite surface protein 1 (msp1) and the circumsporozoite protein (csp) of P. falciparum and P. vivax populations to examine the patterns of gene flow and population structures among seven sites on five islands in Vanuatu. Genetic diversity was in general higher in P. vivax than P. falciparum from the same site. In P. vivax, high genetic diversity was likely maintained by greater extent of gene flow among sites and among islands. Consistent with the different patterns of gene flow, the proportion of genetic variance found among islands was substantially higher in P. falciparum (28.81–31.23%) than in P. vivax (-0.53–3.99%). Our data suggest that the current island-by-island malaria elimination strategy in Vanuatu, while adequate for P. falciparum elimination, might need to be complemented with more centrally integrated measures to control P. vivax movement across islands.
A Comparison between Conductive and Infrared Devices for Measuring Mean Skin Temperature at Rest, during Exercise in the Heat, and Recovery

Purpose Skin temperature assessment has historically been undertaken with conductive devices affixed to the skin. With the development of technology, infrared devices are increasingly utilised in the measurement of skin temperature. Therefore, our purpose was to evaluate the agreement between four skin temperature devices at rest, during exercise in the heat, and recovery. Methods Mean skin temperature (T-sk) was assessed in thirty healthy males during 30 min rest (24.0 ± 1.2°C, 56 ± 8%), 30 min cycle in the heat (38.0 ± 0.5°C, 41 ± 2%), and 45 min recovery (24.0 ± 1.3°C, 56 ± 9%). T-sk was assessed at four sites using two conductive devices (thermistors, iButtons) and two infrared devices (infrared thermometer, infrared camera). Results Bland–Altman plots demonstrated mean bias ± limits of agreement between the thermistors and iButtons as follows (rest, exercise, recovery): -0.01 ± 0.04, 0.26 ± 0.85, -0.37 ± 0.98°C; thermistors and infrared thermometer: 0.34 ± 0.44, -0.44 ± 1.23, -1.04 ± 1.75°C; thermistors and infrared camera (rest, recovery): 0.83 ± 0.77, 1.88 ± 1.87°C. Pairwise comparisons of T-sk found significant differences (p < 0.05) between thermistors and both infrared devices during resting conditions, and significant differences between the thermistors and all other devices tested during exercise in the heat and recovery. Conclusions These results indicate poor agreement between conductive and infrared devices at rest, during exercise in the heat, and subsequent recovery. Infrared devices may not be suitable for monitoring T-sk in the presence of, or following, metabolic and environmental induced heat stress.
FLIP: Federation support for Long range low power Internet of things Protocols

There is growing interest in the Internet of Things (IoT) and especially Low-Power Wide Area Networks (LPWAN), which are rapidly being rolled-out globally. Within the LPWAN market, LoRaWAN is considered a leading solution which has achieved significant success. Despite the rapid uptake of LoRaWAN, scalability concerns arising from interference and contention are also growing. While the current LoRaWAN protocol includes basic techniques to deal with these problems, recent research has shown that these mechanisms are ineffective at large scale. This paper addresses this problem by proposing FLIP, a novel, fully distributed and open architecture for LoRaWAN, that transforms standard LoRa gateways into a federated network, while preserving the privacy and security properties of the original LoRaWAN architecture. FLIP tackles the scalability limitations of LoRaWAN using consensus-driven and localised resource sharing between gateways, while also providing inherent support for the roaming of LoRa devices across the federation. Critically, the FLIP architecture is fully backwards compatible with all existing LoRa gateways and requires no modifications to the firmware of LoRa end-devices, facilitating its rapid adoption.
Commercially available antibodies can be applied in quantitative multiplexed peptide immunoaffinity enrichment targeted mass spectrometry assays

Immunoaffinity enrichment of peptides coupled to multiple reaction monitoring‐mass spectrometry (immuno‐MRM) enables highly specific, sensitive, and precise quantification of peptides and post‐translational modifications. Major obstacles to developing a large number of immuno‐MRM assays are poor availability of monoclonal antibodies (mAbs) validated for immunoaffinity enrichment of peptides and the cost and lead time of developing the antibodies de novo. Although many thousands of mAbs are commercially offered, few have been tested for application to immunoaffinity enrichment of peptides. In this study, we tested the success rate of using commercially available mAbs for peptide immuno‐MRM assays. We selected 105 commercial mAbs (76 targeting non‐modified “pan” epitopes, 29 targeting phosphorylation) to proteins associated with the DNA damage response network. We found that 8 of the 76 pan (11%) and 5 of the 29 phospho‐specific mAbs (17%) captured tryptic peptides (detected by LC‐MS/MS) of their protein targets from human cell lysates. Seven of these mAbs were successfully used to configure and analytically characterize immuno‐MRM assays. By applying selection criteria upfront, the results indicate that a screening success rate of up to 24% is possible, establishing the feasibility of screening a large number of catalog antibodies to provide readily‐available assay reagents.
Recommendations for a Core Outcome Set for Measuring Standing Balance in Adult Populations: A Consensus-Based Approach

Background Standing balance is imperative for mobility and avoiding falls. Use of an excessive number of standing balance measures has limited the synthesis of balance intervention data and hampered consistent clinical practice. Objective To develop recommendations for a core outcome set (COS) of standing balance measures for research and practice among adults. Methodology A combination of scoping reviews, literature appraisal, anonymous voting and face-to-face meetings with fourteen invited experts from a range of disciplines with international recognition in balance measurement and falls prevention. Consensus was sought over three rounds using pre-established criteria. Data sources The scoping review identified 56 existing standing balance measures validated in adult populations with evidence of use in the past five years, and these were considered for inclusion in the COS. Results Fifteen measures were excluded after the first round of scoring and a further 36 after round two. Five measures were considered in round three. Two measures reached consensus for recommendation, and the expert panel recommended that at a minimum, either the Berg Balance Scale or Mini Balance Evaluation Systems Test be used when measuring standing balance in adult populations. Limitations Inclusion of two measures in the COS may increase the feasibility of potential uptake, but poses challenges for data synthesis. Adoption of the standing balance COS does not constitute a comprehensive balance assessment for any population, and users should include additional validated measures as appropriate. Conclusions The absence of a gold standard for measuring standing balance has contributed to the proliferation of outcome measures. These recommendations represent an important first step towards greater standardization in the assessment and measurement of this critical skill and will inform clinical research and practice internationally.