Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-omics profiling of calcium-induced human keratinocytes differentiation reveals modulation of unfolded protein response signaling pathways

ABSTRACT By proteomic, metabolomic and transcriptomic approaches we shed light on the molecular mechanism by which human keratinocytes undergo to terminal differentiation upon in vitro calcium treatment. Proteomic analysis revealed a selective induction of the ribosomal proteins RSSA, an inhibitor of cell proliferation and inducer of differentiation, HSP 60, a protein folding chaperone and GRP78, an unfolding protein response signal. Additionally, we observed an induction of EF1D, a transcription factor for genes that contain heat-shock responsive elements. Conversely, RAD23, a protein involved in regulating ER-associated protein degradation was down-regulated. All these modifications indicated an ER stress response, which in turn activated the unfolded protein response signaling pathway through ATF4, as confirmed both by the modulation of amino acids metabolism genes, such as XBP1, PDI and GPR78, and by the metabolomic analysis. Finally, we detected a reduction of PDI protein, as confirmed by the increase of oxidized glutathione. Metabolome analysis indicated that glycolysis failed to fuel the Krebs cycle, which continued to decrease during differentiation, at glance with the PPP pathway, allowing NADH production and glutathione reduction. Since unfolded protein response is linked to keratinization, these results may be useful for studying pathological mechanisms as well as potential treatments for different pathological conditions. Abbreviation: UPR, unfolded protein response; HEK, human epidermal keratinocytes; HKGS, human keratinocytes growth factor.
Pitching form evaluation based on elbow position by a monocular camera

Pitching in the correct form is essential for preventing injury and improving skills. It is not easy for athletes and instructors to check whether a pitcher is throwing in the correct form. In this study, we record a pitcher from the direction of the catcher by a monocular camera and estimate the skeleton pose of the pitcher by using OpenPose. We propose a new method to evaluate whether the pitcher can pitch in the correct form by examining the estimated pose. We use SSE(Shoulder, Shoulder, Elbow)-line as an evaluation index. When the upper body of the pitcher faces a batter, the SSE-line should be straight. To find the right frame at which the pitcher body turns squarely to the batter, the distance of the shoulders in a video frame is used. When it becomes the largest, the shape of SSE-line should be measured. Since the motion of the pitcher was fast, we use a 240 fps camera to investigate the relationship between the shape of SSE-line and the shoulder distance. The relationship between the shape of the SSE-line and the shoulder distance with the 240 fps camera was evaluated, and we discussed their pitching properties based on the evaluation.
Usability Heuristics for Tabletop Systems Design

: Tabletops are large interactive displays that enable many users to interact at the same time. These devices have different characteristics than other touchscreen devices, such as smartphones or tablets. They cannot be easily moved to bring the screen closer to the eyes or rotate interface elements, changing the screen to horizontal or vertical, for example. In this context, this paper presents a set of heuristics to be considered in tabletop interface design from the initial planning until validation. Nielsen’s heuristics and others adapted or formalized from Nielsen, as well as researches about tabletop characteristics and user tests, were identified and analyzed to adapt and formalize heuristics to tabletop context. A set of twelve heuristics for tabletop context was created and they were considered to design simulator interfaces. Observing the militaries using them, we have gathered evidence that these heuristics can help designers to think about essential interface characteristics to support users to realize and understand the interface goal and how to interact with it.
Seasonal dynamics in a coastal Vibrio community examined by a rapid clustering method based on 16S rDNA

: A rapid clustering scheme for Vibrio specieswas developed based on the analysis of 16S rDNA, which compriseda group-specific polymerase chain reaction (PCR) and restriction fragmentlength polymorphisms (RFLP) of the PCR-amplified 16S rDNA. The group-specificPCR, using a specific primer Vib1F, clustered the Vibrio speciesinto two large groups: Vib1F+ group and Vib1F– group.The PCR-RFLP, using ScaI and BlnI, further dividedthese groups into smaller groups. Finally, 46 Vibrio speciesand eight related species could be clustered into 14 groups usingthis rapid clustering method. Seasonal dynamics of the Vibrio communityin Yoshimi Bay, Hibiki-nada Sea, Japan, were examined based on therapid clustering method. In both seawater and sediments, the groupcomprised Vibrio parahaemolyticus, Vibrio alginolyticus, Vibriocampbellii, Vibrio carchariae, Vibrio harveyi and Vibrionatriegens and was predominant when the seawater temperaturewas above 20°C, whereas the group of Vibrio splendidus biotypeI and Vibrio lentus was abundant when the temperature wasaround or below 20°C.
Investigation of factors determining genotypic differences in seed yield of non-irrigated and irrigated chickpeas using a physiological model of yield determination

Physiological attributes determining yield, both under drought and under irrigated conditions, of some advanced chickpea lines of recent origin were investigated over two seasons using a physiological model. Total shoot biomass, seed yield, and vegetative (Dv) and reproductive (Dr) durations were measured in field trials in peninsular India and the crop growth rates (C) and the rate of partitioning to seed (p) were estimated. The contribution of model parameters to variations in seed yield were determined by path analysis, and the relationships of the yield determinants with seed yield were obtained by regression techniques. The model was found to be suitable for chickpea, and when the parameters were fitted the model explained 98% of the variation. Irrigation enhanced Dr and C. While C was the major single yield determinant, the combination of C and p in non-irrigated environments explained most of the yield variation. Dv and Dr exhibited a negative relationship while C and p exhibited a positive relationship under drought stress and a negative relationship in the irrigated environment. There were indications of the existence of an optimum Dv for maximum C among the genotypes, suggesting the need to select for optimum duration genotypes. As high values for p and C in severe drought stress and Dr and C in the irrigated environments are advantageous for high yield, it is suggested that separate breeding strategies are needed for different soil water environments.
Arthropod Community Similarity in Clonal Stands of Aspen: A Test of the Genetic Similarity Rule

Abstract: Understanding the factors that affect community composition is essential for community ecology. The genetic similarity rule (GSR) identifies 3 variables (host genetic composition, phytochemistry, and the environment) that could affect community composition. Few studies have determined the relative influence of these variables on community composition. Using path analysis, we found that arthropod community similarity was better explained by geographic (56%) and environmental (32%) distance than genetic distance in clonal aspen (Populus tremuloides). Comparing our data with data from similar studies of poplars (P. fremontii and P. fremontii × P. angustifolia hybrids), we found that hybrid poplar stands had higher levels of genetic and arthropod diversity than did clonal aspen stands. We found a significant relationship between genetic and arthropod diversity only in hybrid stands and across Populus systems. Our findings agree with the GSR expectations that the importance of the genetic composition of the host in structuring communities depends in part on the amount of genetic variation present in the study system. This is relevant for management and restoration strategies of geographically restricted species and of disjunct populations of otherwise widespread species, as these tend to have lower effective population sizes and reduced levels of genetic diversity.
Distribution and abundance of the pelagic processid, Processa pippinae Wicksten & Méndez, 1985 (Decapoda, Caridea, Processidae), collected during the TALUD XIV cruise in the Gulf of California, Mexico, and description of a new genus

The pelagic processid, Processa pippinae Wicksten & Mendez, 1985, has been reported previously as an endemic species in the northern Gulf of California, Mexico. Additional material collected accidentally in a benthic sledge and with a mid-water micronecton net is reported, including a series of small-sized specimens (CL 2.2 mm). The shape of the laterally compressed rostrum of this species varies considerably with size and among adult specimens. Based on several morphological characteristics of P. pippinae, a new genus, Maryprocessa, is proposed. Several unique characteristics separate Maryprocessa new genus from the other five genera of Processidae, including the laterally compressed rostrum overreaching the cornea, unique among the Processidae, the extraordinary long antennal and antennular flagella, the posterior lobe on the dorsal margin of the third abdominal somite, and the long, acute pair of spines on the posterior margin of the sixth abdominal somite.
Current in vitro biofilm-infected chronic wound models for developing new treatment possibilities.

SIGNIFICANCE The prevalence of chronic wounds is increasing worldwide. The most recent estimates suggest that up to 2% of the population in the industrialized countries are affected.1 Recent Advances: During the past few decades, bacterial biofilms have been elucidated as one of the primary reasons why chronic wounds fail to heal.2,3 Critical Issues: There is a lack of direct causation and evidence of the role that biofilms play in persistent wounds, which complicates research on new treatment options, since it is still unknown which factors dominate. For this reason, several different in vitro wound models have been created, that mimic the biofilm infections observed in chronic wounds and other chronic infections. These different models are, amongst other purposes, used to test a variety of wound care products. However, chronic wounds are highly complex, and several different factors must be taken into consideration along with the infection, including physiochemical and human-supplemented factors. Furthermore, the limitations of using in vitro models, such as the lack of a responsive immune system should always be given due consideration. FUTURE DIRECTIONS Present understandings of all the elements and interactions that take place within chronic wounds are incomplete. As our insight of in vivo chronic wounds continues to expand, so too must the in vitro models used to mimic these infections evolve and adapt to new knowledge.
LONG-TERM PATTERNS OF SPATIAL AND TEMPORAL DISTRIBUTION IN THE SEABOB SHRIMP XIPHOPENAEUS KROYERI (DECAPODA: PENAEIDAE) POPULATION IN SOUTHEASTERN BRAZIL

The effect of some environmental factors on the distribution and abundance of different demographic categories of Xiphopenaeus kroyeri (Heller, 1862) was tested for three 12-month periods over 13 years in Ubatuba Bay, Sao Paulo State, southeastern Brazil. Four sites with different characteristics were sampled monthly from January to December 1998, July 2006 to June 2007 and September 2010 to August 2011. Bottom water temperature and salinity samples were taken monthly, and one sediment sample from each site was taken during each period. Although total abundance, as the number of adult males and non-reproductive females did not differ among periods, in 1998 the abundance of juveniles was greater and reproductive females was lower than the other two periods. The high abundance of juveniles in 1998 was associated with the high frequency of optimal temperatures for juvenile’s metabolism and this environmental variable can influence the abundance of individuals among years. Adult shrimp can be established in sites with variations in sediment grain size composition, whereas juveniles are more abundant in sites with finer sand. We suggest that areas with high juvenile abundance in Ubatuba Bay must have controlled exploitation and that the fishery can be focused on the deepest areas, where adults are predominant.
Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching

Soil physiochemical properties are regulated by cropping practices, but little is known about how tillage influences soil microbial community diversity and functions. Here, we assessed soil bacterial community assembly and functional profiles in relation to tillage. Soils, collected in 2018 from a 17-year field experiment in northwestern China, were analyzed using high-throughput sequencing and the PICRUSt approach. The taxonomic diversity of bacterial communities was dominated primarily by the phyla Proteobacteria (32–56%), Bacteroidetes (12–33%), and Actinobacteria (17–27%). Alpha diversity (Chao1, Shannon, Simpson, and operational taxonomic unit (OTU) richness) was highest under no-tillage with crop residue removed (NT). Crop residue retention on the soil surface (NTS) or incorporated into soil (TS) promoted the abundance of Proteobacteria by 16 to 74% as compared to conventional tillage (T). Tillage practices mainly affected the pathways of soil metabolism, genetic information processing, and environmental information processing. Soil organic C and NH4–N were the principal contributors to the diversity and composition of soil microbiota, whereas soil pH, total nitrogen, total P, and moisture had little effect. Our results suggest that long-term conservation practices with no-tillage and crop residue retention shape soil bacterial community composition through modifying soil physicochemical properties and promoting the metabolic function of soil microbiomes.
A lamB expression plasmid for extending the host range of phage λ to other enterobacteria

We have constructed a multicopy plasmid vector (pAMH62) expressing lamB, the gene coding for the phage λ receptor protein in Escherichia coli. In this construction, the lamB structural gene was fused to the ompR promoter of E. coli. The ompR promoter was employed because: (i) it can function in other gram negative bacteria; (ii) it expresses lamB in a multicopy state at a level comparable to that of maltose-induced chromosomal lamB in E. coli. The vector pAMH62 was tested in E. coli and Salmonella typhimurium. In both cases the LamB protein was produced in similar amounts, was properly integrated to the outer membrane and was functional as phage λ receptor. Thus pAMH62 should provide a useful tool for extending the host range of phage λ and λ-derived vectors to other Gram-negative bacteria.
Medical Mobile App Classification Using the National Institute for Health and Care Excellence Evidence Standards Framework for Digital Health Technologies: Interrater Reliability Study

Background Clinical governance of medical mobile apps is challenging, and there is currently no standard method for assessing the quality of such apps. In 2018, the National Institute for Health and Care Excellence (NICE) developed a framework for assessing the required level of evidence for digital health technologies (DHTs), as determined by their clinical function. The framework can potentially be used to assess mobile apps, which are a subset of DHTs. To be used reliably in this context, the framework must allow unambiguous classification of an app’s clinical function. Objective The objective of this study was to determine whether mobile health apps could be reliably classified using the NICE evidence standards framework for DHTs. Methods We manually extracted app titles, screenshots, and content descriptions for all apps listed on the National Health Service (NHS) Apps Library website on July 12, 2019; none of the apps were downloaded. Using this information, 2 mobile health (mHealth) researchers independently classified each app to one of the 4 functional tiers (ie, 1, 2, 3a, and 3b) described in the NICE digital technologies evaluation framework. Coders also answered contextual questions from the framework to identify whether apps were deemed to be higher risk. Agreement between coders was assessed using Cohen κ statistic. Results In total, we assessed 76 apps from the NHS Apps Library. There was classification agreement for 42 apps. Of these, 0 apps were unanimously classified into Tier 1; 24, into Tier 2; 15, into Tier 3a; and 3, into Tier 3b. There was disagreement between coders in 34/76 cases (45%); interrater agreement was poor (Cohen κ=0.32, 95% CI 0.16-0.47). Further investigation of disagreements highlighted 5 main explanatory themes: apps that did not correspond to any tier, apps that corresponded to multiple tiers, ambiguous tier descriptions, ambiguous app descriptions, and coder error. Conclusions The current iteration of the NICE evidence standards framework for DHTs did not allow mHealth researchers to consistently and unambiguously classify digital health mobile apps listed on the NHS app library according to their functional tier.
Detection of 7-Dehydrocholesterol and Vitamin D3 Derivatives in Honey

20(S)-Hydroxyvitamin D3 (20(OH)D3) is an endogenous metabolite produced by the action of CYP11A1 on the side chain of vitamin D3 (D3). 20(OH)D3 can be further hydroxylated by CYP11A1, CYP27A1, CYP24A1 and/or CYP27B1 to several hydroxyderivatives. CYP11A1 also hydroxylates D3 to 22-monohydroxyvitamin D3 (22(OH)D3), which is detectable in the epidermis. 20-Hydroxy-7-dehydrocholesterol (20(OH)-7DHC) has been detected in the human epidermis and can be phototransformed into 20(OH)D3 following the absorption of ultraviolet B (UVB) energy by the B-ring. 20(OH)D3 and its hydroxyderivatives have anti-inflammatory, pro-differentiation and anti-proliferative effects, comparable to 1,25-dihydroxyvitamin D3 (1,25(OH)2D3). Since cytochromes P450 with 20- or 25-hydroxylase activity are found in insects participating in ecdysone synthesis from 7-dehydrocholesterol (7DHC), we tested whether D3-hydroxyderivatives are present in honey, implying their production in bees. Honey was collected during summer in the Birmingham area of Alabama or purchased commercially and extracted and analyzed using LC-MS. We detected a clear peak of m/z = 423.324 [M + Na]+ for 20(OH)D3 corresponding to a concentration in honey of 256 ng/g. We also detected peaks of m/z = 383.331 [M + H − H2O]+ for 20(OH)-7DHC and 25(OH)D3 with retention times corresponding to the standards. We further detected species with m/z = 407.329 [M + Na]+ corresponding to the RT of 7DHC, D3 and lumisterol3 (L3). Similarly, peaks with m/z = 399.326 [M + H − H2O]+ were detected at the RT of 1,25(OH)2D3 and 1,20-dihydroxyvitamin D3 (1,20(OH)2D3). Species corresponding to 20-monohydroxylumisterol3 (20(OH)L3), 22-monohydroxyvitamin D3 (22(OH)D3), 20,23-dihydroxyvitamin D3 (20,23(OH)2D3), 20,24/25/26-dihydroxyvitamin D3 (20,24/25/26(OH)2D3) and 1,20,23/24/25/26-trihydroxyvitamin D3 (1,20,23/24/25/26(OH)3D3) were not detectable above the background. In conclusion, the presence of 7DHC and D3 and of species corresponding to 20(OH)-7DHC, 20(OH)D3, 1,20(OH)2D3, 25(OH)D3 and 1,25(OH)2D3 in honey implies their production in bees, although the precise biochemistry and photochemistry of these processes remain to be defined.
Participle clauses between adverbial and complement

The present paper offers a synchronic and diachronic analysis of integrated participle clauses or IPCs in English, as found in constructions such as the mayor is busy washing his car or many students had trouble finding the correct answer. Typically, IPCs have developed from adverbial participle clauses into complement clauses. Given their adverbial origins, they can occur as complements to predicates that do not normally take nominal direct objects. Synchronically, criteria are discussed for distinguishing IPCs from adverbial clauses, and it is shown that the distinction between IPCs and adverbial participle clauses is non-discrete. Diachronically, the origins of IPCs are traced, showing that IPCs emerged gradually in the course of the Modern English period. It is argued that initially the primary mechanism of change was (analogically-induced) reanalysis, yet at a later stage IPCs began to assert themselves as a category in its own right, spreading to new contexts through analogical extension. Thus, the discussion illustrates how adverbial clauses can turn into complements, and at the same time shows how a new syntactic (if fuzzy) pattern takes shape.
Estimation of Hg(II) in Soil Samples by Bioluminescent Bacterial Bioreporter E. coli ARL1, and the Effect of Humic Acids and Metal Ions on the Biosensor Performance

Mercury is a ubiquitous environmental pollutant of dominantly anthropogenic origin. A critical concern for human health is the introduction of mercury to the food chain; therefore, monitoring of mercury levels in agricultural soil is essential. Unfortunately, the total mercury content is not sufficiently informative as mercury can be present in different forms with variable bioavailability. Since 1990, the use of bioreporters has been investigated for assessment of the bioavailability of pollutants; however, real contaminated soils have rarely been used in these studies. In this work, a bioassay with whole-cell bacterial bioreporter Escherichia coli ARL1 was used for estimation of bioavailable concentration of mercury in 11 soil samples. The bioreporter emits bioluminescence in the presence of Hg(II). Four different pretreatments of soil samples prior to the bioassay were tested. Among them, laccase mediated extraction was found to be the most suitable over water extraction, alkaline extraction, and direct use of water-soil suspensions. Nevertheless, effect of the matrix on bioreporter signal was found to be severe and not possible to be completely eliminated by the method of standard addition. In order to elucidate the matrix role, influences of humic acid and selected metal ions present in soil on the bioreporter signal were tested separately in laboratory solutions. Humic acids were found to have a positive effect on the bioreporter growth, but a negative effect on the measured bioluminescence, likely due to shading and Hg binding resulting in decreased bioavailability. Each of the tested metal ions solutions affected the bioluminescence signal differently; cobalt (II) positively, iron (III) negatively, and the effects of iron (II) and nickel (II) were dependent on their concentrations. In conclusion, the information on bioavailable mercury estimated by bioreporter E. coli ARL1 is valuable, but the results must be interpreted with caution. The route to functional bioavailability bioassay remains long.
Development of a new chemical method for distinguishing between Betulapendula and Betulapubescens in Sweden

High performance liquid chromatography (HPLC) analytical studies of inner bark extractives from a large number of silver birch (Betulapendula Roth) and hairy birch (Betulapubescens Ehrh.) trees revealed the diarylheptanoid glucoside platyphylloside to be present at high levels in B. pendula (20–60 mg/g dry bark) and at low levels in B. pubescens (≤ 0.5 mg/g dry bark). Based on these observations, a new simple and accurate precipitation method to distinguish between B. pendula and B. pubescens has been developed. In a solution of 2,4-dinitrophenylhydrazine, platyphylloside immediately forms an orange precipitate. A similar precipitate is also produced when a piece of B. pendula inner bark is kept for 1 h at room temperature in the same solution. However, no precipitate forms when a sample from B. pubescens is used. The diagnostic value of morphological characters was assessed by comparing the results of species determinations made on a large number of trees (> 1600), both juvenile and mature, using the mor.