Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Sensitive Reflective-Mode Defect Detectors and Dielectric Constant Sensors Based on Open-Ended Stepped-Impedance Transmission Lines

In this paper, reflective-mode phase-variation sensors based on open-ended stepped-impedance transmission lines with optimized sensitivity for their use as defect detectors and dielectric constant sensors are reported. The sensitive part of the sensors consists of either a 90° high-impedance or a 180° low-impedance open-ended sensing line. To optimize the sensitivity, such a sensing line is cascaded to a 90° transmission line section with either low or high characteristic impedance, resulting in a stepped-impedance transmission line configuration. For validation purposes, two different sensors are designed and fabricated. One of the sensors is implemented by means of a 90° high impedance (85 Ω) open-ended sensing line cascaded to a 90° low impedance (15 Ω) transmission line section. The other sensor consists of a 180° 15-Ω open-ended sensing line cascaded to a 90° 85-Ω line. Sensitivity optimization for the measurement of dielectric constants in the vicinity of that corresponding to the Rogers RO4003C substrate (i.e., with dielectric constant 3.55) is carried out. The functionality as a defect detector is demonstrated by measuring the phase-variation in samples consisting of the uncoated Rogers RO4003C substrate (the reference sample) with arrays of holes of different densities.
Veterinary trypanocidal benzoxaboroles are peptidase-activated prodrugs

Livestock diseases caused by Trypanosoma congolense, T. vivax and T. brucei, collectively known as nagana, are responsible for billions of dollars in lost food production annually. There is an urgent need for novel therapeutics. Encouragingly, promising antitrypanosomal benzoxaboroles are under veterinary development. Here, we show that the most efficacious subclass of these compounds are prodrugs activated by trypanosome serine carboxypeptidases (CBPs). Drug-resistance to a development candidate, AN11736, emerged readily in T. brucei, due to partial deletion within the locus containing three tandem copies of the CBP genes. T. congolense parasites, which possess a larger array of related CBPs, also developed resistance to AN11736 through deletion within the locus. A genome-scale screen in T. brucei confirmed CBP loss-of-function as the primary mechanism of resistance and CRISPR-Cas9 editing proved that partial deletion within the locus was sufficient to confer resistance. CBP re-expression in either T. brucei or T. congolense AN11736-resistant lines restored drug-susceptibility. CBPs act by cleaving the benzoxaborole AN11736 to a carboxylic acid derivative, revealing a prodrug activation mechanism. Loss of CBP activity results in massive reduction in net uptake of AN11736, indicating that entry is facilitated by the concentration gradient created by prodrug metabolism.
Single-Molecule Counting of Nucleotide by Electrophoresis with Nanochannel-Integrated Nano-Gap Devices

We utilized electrophoresis to control the fluidity of sample biomolecules in sample aqueous solutions inside the nanochannel for single-molecule detection by using a nanochannel-integrated nanogap electrode, which is composed of a nano-gap sensing electrode, nanochannel, and tapered focusing channel. In order to suppress electro-osmotic flow and thermal convection inside this nanochannel, we optimized the reduction ratios of the tapered focusing channel, and the ratio of inlet 10 μm to outlet 0.5 μm was found to be high performance of electrophoresis with lower concentration of 0.05 × TBE (Tris/Borate/EDTA) buffer containing a surfactant of 0.1 w/v% polyvinylpyrrolidone (PVP). Under the optimized conditions, single-molecule electrical measurement of deoxyguanosine monophosphate (dGMP) was performed and it was found that the throughput was significantly improved by nearly an order of magnitude compared to that without electrophoresis. In addition, it was also found that the long-duration signals that could interfere with discrimination were significantly reduced. This is because the strong electrophoresis flow inside the nanochannels prevents the molecules’ adsorption near the electrodes. This single-molecule electrical measurement with nanochannel-integrated nano-gap electrodes by electrophoresis significantly improved the throughput of signal detection and identification accuracy.
Artificial intelligence for the measurement of vocal stereotypy

Both researchers and practitioners often rely on direct observation to measure and monitor behavior. When these behaviors are too complex or numerous to be measured in vivo, relying on direct observation using human observers increases the amount of resources required to conduct research and to monitor the effects of interventions in practice. To address this issue, we conducted a proof of concept examining whether artificial intelligence could measure vocal stereotypy in individuals with autism. More specifically, we used an artificial neural network with over 1,500 minutes of audio data from 8 different individuals to train and test models to measure vocal stereotypy. Our results showed that the artificial neural network performed adequately (i.e., session‐by‐session correlation near or above .80 with a human observer) in measuring engagement in vocal stereotypy for 6 of 8 participants. Additional research is needed to further improve the generalizability of the approach.
Cardiac pathology in mucopolysaccharidosis I mice: Losartan modifies ERK1/2 activation during cardiac remodeling

Mucopolysaccharidosis type I (MPS I) is a lysosomal storage disorder caused by mutations in the IDUA gene, that codifies the alpha‐L‐iduronidase enzyme, which deficiency leads to storage of glycosaminoglycans, with multiple clinical manifestations. One of the leading causes of death in MPS I patients are cardiac complications such as cardiac valve thickening, conduction abnormalities, myocardial dysfunction, and cardiac hypertrophy. The mechanism leading to cardiac dysfunction in MPS I is not entirely understood. In a previous study, we have demonstrated that losartan and propranolol improved the cardiac function in MPS I mice. Thus, we aimed to investigate whether the pathways influenced by these drugs may modulate the cardiac remodeling process in MPS I mice. According to our previous observation, losartan and propranolol restore the heart function, without altering valve thickness. MPS I mice presented reduced activation of AKT and ERK1/2, increased activity of cathepsins, but no alteration in metalloproteinase activity was observed. Animals treated with losartan showed a reduction in cathepsin activity and restored ERK1/2 activation. While both losartan and propranolol improved heart function, no mechanistic evidence was found for propranolol so far. Our results suggest that losartan or propranolol could be used to ameliorate the cardiac disease in MPS I and could be considered as adjuvant treatment candidates for therapy optimization.
Pheno-RNA, a method to associate genes with a specific phenotype, identifies genes linked to cellular transformation

Significance Pheno-RNA is a new idea/method to identify genes important for a phenotype. It involves 1) generating a phenotypic series that involves different experimental conditions to yield a measurable phenotype, 2) performing transcriptional profiling under all the conditions, and 3) correlating gene expression profiles with phenotypic strength. Using this method, we identified ∼200 genes whose expression profiles over 17 conditions show a remarkably high correlation to the level of transformation. As expected, these ∼200 genes are enriched in biological categories important for transformation. Within these categories, some genes have very high correlations with the transformation phenotype, whereas others do not. Ninety genes with high correlations have not been previously linked to cancer, suggesting heretofore unknown genes with a role in cancer. Cellular transformation is associated with dramatic changes in gene expression, but it is difficult to determine which regulated genes are oncogenically relevant. Here we describe Pheno-RNA, a general approach to identifying candidate genes associated with a specific phenotype. Specifically, we generate a “phenotypic series” by treating a nontransformed breast cell line with a wide variety of molecules that induce cellular transformation to various extents. By performing transcriptional profiling across this phenotypic series, the expression profile of every gene can be correlated with the strength of the transformed phenotype. We identify ∼200 genes whose expression profiles are very highly correlated with the transformation phenotype, strongly suggesting their importance in transformation. Within biological categories linked to cancer, some genes show high correlations with the transformed phenotype, but others do not. Many genes whose expression profiles are highly correlated with transformation have never been associated with cancer, suggesting the involvement of heretofore unknown genes in cancer.
Vulnerability to climate change for narrowly ranged species: the case of Ecuadorian endemic Magnolia mercedesiarum

Species vulnerability to climate change has been inferred using species distribution models from an example of the recently discovered Magnolia mercedesiarum (sect. Talauma, Magnoliaceae), a narrowly ranged species endemic to moist tropical forests in the eastern Ecuadorian Andes. The environmental conditions within the current species distribution area has been compared with conditions projected to 2050 and 2070, using data from the HadGEM2-ES model in two CO2 emission scenarios: RCP4.5 and RCP8.5. The ecological niche modelling allowed determination of parameters of climatic environmental conditions that control current species distribution to produce a hypothesis on probable changes in spatial pattern of suitable habitats in future scenarios. Within the current species distribution area of M. mercedesiarum, significant reduction of habitat suitability was projected for both emission scenarios, combined with a lack of nearby areas with adequate environmental conditions. Several disjunct sites of high habitat suitability were found to emerge in the Colombian Andes, but they seem unreachable by this tree species in the scope of a few decades, due to intrinsic dispersal limitations. The reduction of habitat suitability and improbability of distribution area shift to adjacent geographic locations could mean a high species vulnerability to climate change. The species could be at risk of extinction if it does not possess hidden phenotypical plasticity and potential for fast adaptation to climate change.
Elevated serum granzyme B levels are associated with disease activity and joint damage in patients with rheumatoid arthritis

Objectives Little is known about the roles of granzyme B in rheumatoid arthritis (RA). We aimed to evaluate the serum level of granzyme B in patients with RA and determine relationships with clinical features and joint destruction of RA. Methods We enrolled 100 patients with RA, 50 patients with osteoarthritis (OA), and 50 healthy controls (HC). Granzyme B serum concentrations were measured by ELISA; we then analyzed associations between granzyme B levels, clinical features, and joint destruction by calculating Sharp scores and disease activity as measured by Disease Activity Score-28 based on erythrocyte sedimentation rate (DAS28-ESR) in patients with RA. Results Compared with HC and patients with OA, serum granzyme B levels in patients with RA were remarkably elevated. Serum granzyme B levels did not differ between patients with OA and HC. Granzyme B levels correlated with ESR, rheumatoid factor, swollen joint counts, joint erosion scores, total Sharp scores, and DAS28-ESR. Moreover, patients with RA with high disease activity had higher granzyme B levels. Conclusions Serum granzyme B levels were elevated significantly in patients with RA and correlated positively with disease activity and joint destruction. Serum granzyme B may have potential applications in laboratory evaluation of patients with RA.
Stability of Chlorophyll a Monomer Incorporated into Cremophor EL Nano-Micelles under Dark and Moderate Light Conditions

In this paper, stability of chlorophyll a monomers encapsulated into the Cremophor EL nano-micelles was studied under dark and moderate light conditions, typical of a room with natural or artificial lighting, in the presence of oxygen. The pigment stability against visible light was determined using the dynamic light scattering and molecular spectroscopy (UV-Vis absorption and stationary fluorescence) methods. Chlorophyll a, at the molar concentration of 10−5 M, was dissolved in the 5 wt% Cremophor emulsion for comparison in the ethanolic solution. The stability of such a self-assembly pigment–detergent nano-system is important in the light of its application on the commercial-scale. The presented results indicate the high stability of the pigment monomeric molecular organization in the nano-emulsion. During the storage in the dark, the half-lifetime was calculated as about 7 months. Additionally, based on the shape of absorption and fluorescence emission spectra, chlorophyll aggregation in the Cremophor EL aqueous solution along with the time was excluded. Moreover, the average size of detergent micelles as chlorophyll carriers was not affected after 70 days of the nano-system storage. Pigment stability against the moderate white light (0.1 mW) did not differ significantly from storage conditions in the dark. The photooxidation products, detected by occurrence of new absorption and fluorescence emission bands, was estimated on the negligible level. The stability of such a self-assembly pigment–detergent nano-system would potentially broaden the field of chlorophyll a (chl a) application in the food industry, medicine or artificial photosynthesis models.
Comorbidity in Older Patients Hospitalized with Cancer in Northeast China based on Hospital Discharge Data

Patients with cancer often carry the dual burden of the cancer itself and other co-existing medical conditions. The problems associated with comorbidities among elderly cancer patients are more prominent compared with younger patients. This study aimed to identify common cancer-related comorbidities in elderly patients through routinely collected hospital discharge data and to use association rules to analyze the prevalence and patterns of these comorbidities in elderly cancer patients at different cancer sites. We collected the discharge data of 80,574 patients who were diagnosed with cancers of the esophagus, stomach, colorectum, liver, lung, female breast, cervix, and thyroid between 2016 and 2018. The same number of non-cancer patients were randomly selected as the control group and matched with the case group by age and gender. The results showed that cardiovascular diseases, metabolic diseases, digestive diseases, and anemia were the most common comorbidities in elderly patients with cancer. The comorbidity patterns differed based on the cancer site. Elderly patients with liver cancer had the highest risk of comorbidities, followed by lung cancer, gastrointestinal cancer, thyroid cancer, and reproductive cancer. For example, elderly patients with liver cancer had the higher risk of the comorbid infectious and digestive diseases, whereas patients with lung cancer had the higher risk of the comorbid respiratory system diseases. The findings can assist clinicians in diagnosing comorbidities and contribute to the allocation of medical resources.
Dimensionality Reduction for Tensor Data Based on Local Decision Margin Maximization

In machine learning, the idea of maximizing the margin between two classes is widely used in classifier design. Enlighted by the idea, this paper proposes a novel supervised dimensionality reduction method for tensor data based on local decision margin maximization. The proposed method seeks to preserve and protect the local discriminant information of the original data in the low-dimensional data space. Firstly, we depart the original tensor dataset into overlapped localities with discriminant information. Then, we extract the similarity and anti-similarity coefficients of each high-dimensional locality and preserve these coefficients in the embedding data space via the multilinear projection scheme. Under the combined effect of these coefficients, each dimension-reduced locality tends to be a convex set where strongly correlated intraclass points gather. Simultaneously, the local decision margin, which is defined as the shortest distance from the boundary of each locality to the nearest point of each side, will be maximized. Therefore, the local discriminant structure of the original data could be well maintained in the low-dimensional data space. Moreover, a simple iterative scheme is proposed to solve the final optimization problem. Finally, the experiment results on 6 real-world datasets demonstrate the effectiveness of the proposed method.
New RNA Structural Elements Identified in the Coding Region of the Coxsackie B3 Virus Genome

Here we present a set of new structural elements formed within the open reading frame of the virus, which are highly probable, evolutionarily conserved and may interact with host proteins. This work focused on the coding regions of the CVB3 genome (particularly the V4-, V1-, 2C-, and 3D-coding regions), which, with the exception of the cis-acting replication element (CRE), have not yet been subjected to experimental analysis of their structures. The SHAPE technique, chemical modification with DMS and RNA cleavage with Pb2+, were performed in order to characterize the RNA structure. The experimental results were used to improve the computer prediction of the structural models, whereas a phylogenetic analysis was performed to check universality of the newly identified structural elements for twenty CVB3 genomes and 11 other enteroviruses. Some of the RNA motifs turned out to be conserved among different enteroviruses. We also observed that the 3′-terminal region of the genome tends to dimerize in a magnesium concentration-dependent manner. RNA affinity chromatography was used to confirm RNA–protein interactions hypothesized by database searches, leading to the discovery of several interactions, which may be important for virus propagation.
Habitat-scale heterogeneity maintains fungal endophyte diversity in two native prairie legumes

ABSTRACT The assembly of fungal endophyte communities within plants depends on the complex interactions of fungal taxa, their host plants, and the abiotic environment. Prairie plant communities provide a unique avenue to explore the interplay of biotic and abiotic factors affecting endophyte communities, since the historical distribution of prairies spans a broad range of temperature and precipitation, while the distances between small fragments of contemporary prairie communities may challenge the dispersal capabilities of these otherwise ubiquitous fungi. We sampled foliar fungal endophytes from two native prairie legumes, purple and white prairie clovers (Dalea purpurea and D. candida), in 17 remnant prairie sites across Minnesota in order to evaluate the relative contributions of abiotic factors, host species, and dispersal limitation to the diversity and structure of these communities. We found that similarity of communities was significantly associated with their location along a temperature and precipitation gradient, and we showed a distance-decay relationship that suggests dispersal limitations only over very large spatial scales. Although the effect of host species was small relative to these other factors, the two Dalea species maintained distinct communities within sites where they co-occur. Our results illustrate the capacity of many of these endophyte taxa to disperse over large distances and across heterogeneous biotic and abiotic environments and suggest that the interplay of biotic and abiotic factors maintains high diversity observed in endophyte communities.
Investigating The Life Cycle of Haplosporidium Nelsoni (Msx): A Review

ABSTRACT Attempts to decipher the life cycle of Haplosporidium nelsoni began almost immediately after it was identified as the pathogen causing MSX disease in eastern oysters, Crassostrea virginica. But transmission experiments failed and the spore stage, characteristic of haplosporidans, was extremely rare. Researchers concluded that another host was involved: an intermediate host in which part of the life cycle was produced, or—if the oyster was an accidental host—an alternate host that produces infective elements. A later finding that spores were found more often in spat (<1 y old) than in adults revived the idea of direct transmission between oysters. The new findings and the availability of molecular diagnostics led us to revive life cycle investigations. Over several years, oyster spat were examined for spores and searched for H. nelsoni in potential non-oyster hosts using both histological and polymerase chain reaction (PCR) methodologies. Although spores occurred in a high proportion of spat with advanced infections, it was concluded that they were unlikely to be a principal source of infective elements because naïve oysters used as sentinels to assess infection pressure became highly infected even after native oysters developed resistance, and infected spat could no longer be found. A histological survey of zooplankton and small bivalves in Delaware Bay found few recognizable parasites and nothing resembling a haplosporidan. A subsequent PCR study of water, sediment, and macroinvertebrates from Chesapeake, Delaware, and Oyster bays resulted in many positive samples, but in situ hybridization failed to identify any recognizable structures. PCR analysis of potential intermediate hosts for other molluscan pathogens has also resulted in many species yielding positive results but required in situ hybridization to verify infections. It is suggested that any future search for a nonoyster host of H. nelsoni be conducted in a relatively confined system and/or target specific phyla, strategies that have been successful in other life cycle studies. It is noted that candidate phyla could include those known to host haplosporidans and species whose abundance or distribution may have changed in concert with outbreaks of MSX disease in the northeastern United States in recent years.
Child disability and caregiving in low and middle income countries: Big data approach on open data.

BACKGROUND The presence of child disabilities might affect the amount of caregiving attention the child receives, with potential ramifications on the development of the child and increasing the likelihood of developing a more severe condition. Little is known about the association between child disabilities and caregiving practices in less developed countries, penalized by both lack of data and a research bias toward western societies. METHOD In this study, we apply data mining methods on a large (N = 29,525) dataset from UNICEF to investigate the association between caregiving practices and developmental disabilities of the children, and highlight the differences between intellectual and other disabilities. RESULTS Our results highlight that, compared to other types of disabilities, intellectual disabilities increased the risk of being neglected by the caregiver in those activities oriented to the cognitive development. The education of the caregiver and the socioeconomical development of the country are actively involved in the moderation of the risk. CONCLUSION We demonstrated that educational policies of parental training, such as psychoeducation regarding intellectual disabilities and destigmatization campaigns, are needed to benefit parental practices in low- and middle-income countries.