Miracle-dz/UniFAR-FTUs huggingface dataset:
Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification

Mass spectrometry‐based proteomics is a popular and powerful method for precise and highly multiplexed protein identification. The most common method of analyzing untargeted proteomics data is called database searching, where the database is simply a collection of protein sequences from the target organism, derived from genome sequencing. Experimental peptide tandem mass spectra are compared to simplified models of theoretical spectra calculated from the translated genomic sequences. However, in several interesting application areas, such as forensics, archaeology, venomics, and others, a genome sequence may not be available, or the correct genome sequence to use is not known. In these cases, de novo peptide identification can play an important role. De novo methods infer peptide sequence directly from the tandem mass spectrum without reference to a sequence database, usually using graph‐based or machine learning algorithms. In this review, we provide a basic overview of de novo peptide identification methods and applications, briefly covering de novo algorithms and tools, and focusing in more depth on recent applications from venomics, metaproteomics, forensics, and characterization of antibody drugs.
Comparison of acid-soluble collagen characteristic from three important freshwater fish skins in Mekong Delta Region, Vietnam.

The utilization of three important freshwater fish skins including tra catfish (Pangasianodon hypophthalmus), clown knifefish (Chitala ornata), and tilapia (Oreochromis niloticus) in Mekong Delta Region, Vietnam for acid-soluble collagen (ASC) extraction was investigated. From the SDS-PAGE profile, ASCs can be identified as type I collagen (consisting of two different α- chains and β component in protein pattern). The solubility among individual collagens was highest at pH 1-2, depending on fish species. FTIR spectra showed a close relationship between the lowest wavelength number in amide I and amide III regions and the stabilization of the triple-helical structure in ASC from clown knifefish. ASC from clown knifefish skin had highest ASC yield and contained highest amino acid content as well as the highest denaturation temperature (33.09°C) in comparison with ASCs from tra catfish and tilapia skin. PRACTICAL APPLICATIONS: Acid-soluble collagen (ASC) from three important fish skins in the Mekong Delta Region, Vietnam was characterized. ASC from clown knifefish skin showed the highest of extraction yield and denaturation temperature. The thermal stability of ASC from clown knifefish skin not only related to the content of imino acid but is also had the correlation with the transition of α-helix in amide I and III.
Fine Art Photography: A New Perspective in Documenting Architecture

Nowadays, our environment surrounded by thousands of images. Images are essential in human communication then, it can be viewed from a verity of form and style. Thereby, this research intended to explore the perspective of fine art photography in documenting the architecture. Masjid Ubaidah, Kuala Kangsar was selected as the case study to implement this new perspective of photograph specifically. This study was conducted using qualitative research where the design process was involved in visual research analysis. The structure observation was carried out to identify the common style used by photographer in producing the images of Masjid Ubaidah, Kuala Kangsar and how the creativity and aesthetic value can be built by injecting the fine art approach. This research found that the potential for fine art approach as a new method in documenting Masjid Ubaidah, Kuala Kangsar by establishing the diversity of creativity in aesthetic discussion.
The Role of Animacy in Children's Interpretation of Relative Clauses in English: Evidence From Sentence-Picture Matching and Eye Movements

Subject relative clauses (SRCs) are typically processed more easily than object relative clauses (ORCs), but this difference is diminished by an inanimate head-noun in semantically non-reversible ORCs ("The book that the boy is reading"). In two eye-tracking experiments, we investigated the influence of animacy on online processing of semantically reversible SRCs and ORCs using lexically inanimate items that were perceptually animate due to motion (e.g., "Where is the tractor that the cow is chasing"). In Experiment 1, 48 children (aged 4;5-6;4) and 32 adults listened to sentences that varied in the lexical animacy of the NP1 head-noun (Animate/Inanimate) and relative clause (RC) type (SRC/ORC) with an animate NP2 while viewing two images depicting opposite actions. As expected, inanimate head-nouns facilitated the correct interpretation of ORCs in children; however, online data revealed children were more likely to anticipate an SRC as the RC unfolded when an inanimate head-noun was used, suggesting processing was sensitive to perceptual animacy. In Experiment 2, we repeated our design with inanimate (rather than animate) NP2s (e.g., "where is the tractor that the car is following") to investigate whether our online findings were due to increased visual surprisal at an inanimate as agent, or to similarity-based interference. We again found greater anticipation for an SRC in the inanimate condition, supporting our surprisal hypothesis. Across the experiments, offline measures show that lexical animacy influenced children's interpretation of ORCs, whereas online measures reveal that as RCs unfolded, children were sensitive to the perceptual animacy of lexically inanimate NPs, which was not reflected in the offline data. Overall measures of syntactic comprehension, inhibitory control, and verbal short-term memory and working memory were not predictive of children's accuracy in RC interpretation, with the exception of a positive correlation with a standardized measure of syntactic comprehension in Experiment 1.
Pediatric case of lichen planus pigmentosus inversus successfully treated with narrow band ultraviolet B phototherapy

Dear Editor, Lichen planus (LP) pigmentosus inversus (LPPI) is a variant of LP, presenting with hyperpigmented macules, papules and patches located primarily in intertriginous areas. It is an infrequent entity, with less than 50 cases reported in the literature. LPPI in the pediatric age group is extremely rare with only three cases reported in literature. We present a pediatric case of LPPI successfully treated with narrow band ultraviolet B (NB-UVB) phototherapy. A 13-year-old otherwise healthy boy presented with a 6-month history of mildly pruritic hyperpigmented spots in his skin folds. He had been refractive to various topical corticosteroids and antifungal creams. Dermatological examination revealed dark-brown macules and patches located on the neck, back, inner side of the thighs and cubital, axillary and inguinal folds (Figure 1A,C). Scalp, skin appendages and mucosae were spared. Wood's lamp examination showed no fluorescence, and the potassium hydroxide preparation was negative for fungal elements. Laboratory evaluation was normal, including a negative hepatitis C antibody test. Dermoscopy findings revealed gray to brown colored dots and globules on a diffuse yellow-brown background, and perifollicular pigment deposits (Figure 2A).
Crystal structure of a GH1 β‐glucosidase from Hamamotoa singularis

A GH1 β‐glucosidase from the fungus Hamamotoa singularis (HsBglA) has high transgalactosylation activity and efficiently converts lactose to galactooligosaccharides. Consequently, HsBglA is among the most widely used enzymes for industrial galactooligosaccharide production. Here, we present the first crystal structures of HsBglA with and without 4′‐galactosyllactose, a tri‐galactooligosaccharide, at 3.0 and 2.1 Å resolutions, respectively. These structures reveal details of the structural elements that define the catalytic activity and substrate binding of HsBglA, and provide a possible interpretation for its high catalytic potency for transgalactosylation reaction.
Comparison of semi-quantitative and quantitative methods for diagnosis of catheter-related blood stream infections: a systematic review and meta-analysis of diagnostic accuracy studies

Abstract Catheter-related blood-stream infections (CRBSIs) are the most common healthcare-associated blood-stream infections. They can be diagnosed by either semi-quantitative or quantitative methods, which may differ in diagnostic accuracy. A meta-analysis was undertaken to compare the diagnostic accuracy of semi-quantitative and quantitative methods for CRBSI. A systematic search of Medline, Scopus, Cochrane and Embase databases up to January 2020 was performed and subjected to a QUADAS (quality assessment of diagnostic accuracy studies 2) tool to evaluate the risk of bias among studies. The pooled sensitivity and specificity of the methods were determined and heterogeneity was evaluated using the χ2 test and I2. Publication bias was assessed using a Funnel plot and the Egger's test. In total, 45 studies were analysed with data from 11 232 patients. The pooled sensitivity and specificity of semi-quantitative methods were 85% (95% CI 79–90%) and 84% (95% CI 79–88%), respectively; and for quantitative methods were 85% (95% CI 79–90%) and 95% (95% CI 91–97%). Considerable heterogeneity was statistically evident (P < 0.001) by both methods with a correspondingly symmetrical Funnel plot that was confirmed by a non-significant Deek's test. We conclude that both semi-quantitative and quantitative methods are highly useful for screening for CRBSI in patients and display high sensitivity and specificity. Quantitative methods, particularly paired quantitative cultures, had the highest sensitivity and specificity and can be used to identify CRBSI cases with a high degree of certainty.
The App Store Model for Enterprise Application Software

App stores in the consumer software market are omnipresent and have significantly changed the way how software is being produced, marketed, and consumed. Enterprise software customers also demand higher flexibility in buying and adopting standardized enterprise application software - and new technologies such as cloud computing and highly efficient development platforms provide new options for software vendors and the entire software value chain. This application-oriented work researches the challenge of establishing the app store model for enterprise application software as a technology-driven business model in a two-sided platform ecosystem. The author analyzes the topic comprehensively from the software buyer’s, the software provider’s and the platform provider’s perspective and uncovers detailed insights on barriers, drivers, and constraints. Moreover he proposes solutions on the level business processes and detailed requirements. His research is highly interdisciplinary and utilizes both empirical qualitative and design-oriented methods.
A quantitative modelling approach to zebrafish pigment pattern formation

Pattern formation is a key aspect of development. Adult zebrafish exhibit a striking striped pattern generated through the self-organisation of three different chromatophores. Numerous investigations have revealed a multitude of individual cell-cell interactions important for this self-organisation, but it has remained unclear whether these known biological rules were sufficient to explain pattern formation. To test this, we present an individual-based mathematical model incorporating all the important cell-types and known interactions. The model qualitatively and quantitatively reproduces wild type and mutant pigment pattern development. We use it to resolve a number of outstanding biological uncertainties, including the roles of domain growth and the initial iridophore stripe, and to generate hypotheses about the functions of leopard. We conclude that our rule-set is sufficient to recapitulate wild-type and mutant patterns. Our work now leads the way for further in silico exploration of the developmental and evolutionary implications of this pigment patterning system.
Endothelial Nitric Oxide Suppresses Action-Potential-Like Transient Spikes and Vasospasm in Small Resistance Arteries

Supplemental Digital Content is available in the text. Endothelial dysfunction in small arteries is a ubiquitous, early feature of cardiovascular disease, including hypertension. Dysfunction reflects reduced bioavailability of endothelium-derived nitric oxide (NO) and depressed endothelium-dependent hyperpolarization that enhances vasoreactivity. We measured smooth muscle membrane potential and tension, smooth muscle calcium, and used real-time quantitative polymerase chain reaction in small arteries and isolated tubes of endothelium to investigate how dysfunction enhances vasoreactivity. Rat nonmyogenic mesenteric resistance arteries developed vasomotion to micromolar phenylephrine (α1-adrenoceptor agonist); symmetrical vasoconstrictor oscillations mediated by L-type voltage-gated Ca2+ channels (VGCCs). Inhibiting NO synthesis abolished vasomotion so nanomolar phenylephrine now stimulated rapid, transient depolarizing spikes in the smooth muscle associated with chaotic vasomotion/vasospasm. Endothelium-dependent hyperpolarization block also enabled phenylephrine-vasospasm but without spikes or chaotic vasomotion. Depolarizing spikes were Ca2+-based and abolished by either T-type or L-type VGCCs blockers with depressed vasoconstriction. Removing NO also enabled transient spikes/vasoconstriction to Bay K-8644 (L-type VGCC activator). However, these were abolished by the L-type VGCC blocker nifedipine but not T-type VGCC block. Phenylephrine also initiated T-type VGCC-transient spikes and enhanced vasoconstriction after NO loss in nonmyogenic arteries from spontaneously hypertensive rats. In contrast to mesenteric arteries, myogenic coronary arteries displayed transient spikes and further vasoconstriction spontaneously on loss of NO. T-type VGCC block abolished these spikes and additional vasoconstriction but not myogenic tone. Therefore, in myogenic and nonmyogenic small arteries, reduced NO bioavailability engages T-type VGCCs, triggering transient depolarizing spikes in normally quiescent vascular smooth muscle to cause vasospasm. T-type block may offer a means to suppress vasospasm without inhibiting myogenic tone mediated by L-type VGCCs.
Optical imaging of collagen fiber damage to assess thermally injured human skin

Surgery is the definitive treatment for burn patients who sustain full‐thickness burn injuries. Visual assessment of burn depth is made by the clinician early after injury but is accurate only up to 70% of the time among experienced surgeons. Collagen undergoes denaturation as a result of thermal injury; however, the association of collagen denaturation and cellular death in response to thermal injury is unknown. While gene expression assays and histologic staining allow for ex vivo identification of collagen changes, these methods do not provide spatial or integrity information in vivo. Thermal effects on collagen and the role of collagen in wound repair have been understudied in human burn models due to a lack of methods to visualize both intact and denatured collagen. Hence, there is a critical need for a clinically applicable method to discriminate between damaged and intact collagen fibers in tissues. We present two complementary candidate methods for visualization of collagen structure in three dimensions. Second harmonic generation imaging offers a label‐free, high‐resolution method to identify intact collagen. Simultaneously, a fluorophore‐tagged collagen‐mimetic peptide can detect damaged collagen. Together, these methods enable the characterization of collagen damage in human skin biopsies from burn patients, as well as ex vivo thermally injured human skin samples. These combined methods could enhance the understanding of the role of collagen in human wound healing after thermal injury and potentially assist in clinical decision‐making.
Seed Germination Ecology of Junglerice (Echinochloa colona): A Major Weed of Rice

Abstract Junglerice is one of the most serious grass weeds of rice in the tropics. Experiments were conducted in the laboratory and screenhouse to determine the influence of environmental factors on seed germination and seedling emergence of junglerice in the Philippines. In the laboratory, germination was stimulated by light, suggesting that seeds of this species are positively photoblastic. The tested temperatures (35/25, 30/20, and 25/15 C alternating day/night temperatures), however, did not influence germination. Germination in the laboratory was not affected by a soil pH range of 4 to 9, but was decreased by salinity (> 50 mM NaCl) and moisture stress (< −0.2 MPa osmotic potential). In the screenhouse, germination of junglerice was greatest (97%) for seeds at the soil surface, but emergence declined exponentially with increasing seed burial depth, and no seedlings emerged from seeds buried at 6 cm. In pots, seedling emergence declined markedly with the addition of rice residue to the soil surface at rates equivalent to 4 to 6 tonnes (t) ha−1. As germination of junglerice was strongly stimulated by light, and seedling emergence was optimal at shallow burial depths, this species is likely to be problematic in reduced tillage systems. Nomenclature: Junglerice, Echinochloa colona (L.) Link ECHCO; rice, Oryza sativa L.
In vivo interpretation of model predicted inhibition in acrylate pathway engineered Lactococcus lactis

To maximize the productivity of engineered metabolic pathway, in silico model is an established means to provide features of enzyme reaction dynamics. In our previous study, Escherichia coli engineered with acrylate pathway yielded low propionic acid titer. To understand the bottleneck behind this low productivity, a kinetic model was developed that incorporates the enzymatic reactions of the acrylate pathway. The resulting model was capable of simulating the fluxes reported under in vitro studies with good agreement, suggesting repression of propionyl‐CoA transferase (Pct) by carboxylate metabolites as the main limiting factor for propionate production. Furthermore, the predicted flux control coefficients of the pathway enzymes under steady state conditions revealed that the control of flux is shared between Pct and lactoyl‐CoA dehydratase. Increase in lactate concentration showed gradual decrease in flux control coefficients of Pct that in turn confirmed the control exerted by the carboxylate substrate. To interpret these in silico predictions under in vivo system, an organized study was conducted with a lactic acid bacteria strain engineered with acrylate pathway. Analysis reported a decreased product formation rate on attainment of inhibitory titer by suspected metabolites and supported the model.
Management of massive subcutaneous emphysema with a surgical tracheostomy

Introduction: Interventions for massive subcutaneous emphysema is rarely reported in the literature with lack of comparative studies and strong preferences over one treatment option compared to another. Tracheostomy is a conservative measure as compared to primary closure of tracheobronchial injury for the management of massive subcutaneous emphysema.Case report: A 62-year gentleman who developed massive subcutaneous emphysema on the 12th post-operative day following two laparoscopic abdominal surgeries and an exploratory laparotomy. A computer tomographic scan was performed showing a suspicious tenting of the trachea at right posterolateral wall at the level of T2 vertebra with locules of air seen anterolaterally to the trachea. A subsequent microlaryngobronchoscopy performed showed no defect in the subglottic region, nor tracheobronchial tree. He was successfully managed with a surgical tracheostomy whereby the emphysema showed dramatic resolution on the second postoperative day.Conclusion: Surgical tracheostomy demonstrated a success in managing massive subcutaneous emphysema.
Burning effects on detritivory and litter decay in Campos grasslands

Disturbances are primary forces creating spatial heterogeneity in ecosystems, and inducing changes on biological communities, abiotic characteristics and ecological processes. Here we focus on the effects of fire disturbance in the decomposition process at subtropical Campos grasslands in South Brazil, where burns are traditionally used to reduce shrub encroachment, and improve forage quality. We experimentally investigated how burns and the changes they produce in grassland habitat conditions affect soil fauna detritivory and surface leaf-litter decaying patterns over one year. Previously to fire, we found significant correlation of litter decay with plant evenness and detritivory rates in non-disturbed grasslands. One month after fire grassland patches presented reduced soil fauna densities and surface feeding activity possible because of the mortality caused directly by heating, and/or due to harsh microenvironmental filters to fauna colonization and permanency (e.g. decreased humidity). At 6–7 months after fire however these features did not differ any more from the paired unburned plots. On the other hand, canopy openness accelerated the decaying of leaf-litter in burned patches by allowing increased action of abiotic factors as solar radiation potentially triggering photodegradation. These effects seemed to last less than one year. Overall, our results bring insights regarding drivers of soil ecological processes at local scales in subtropical grasslands, and suggest that detritivory and litter decay processes are sensitive to fire, but resilient following grassland recovering.
Recent Data to the Knowledge of the Aphid Fauna of Hungary (Homoptera: Aphidoidea)

A report on the partial results of the regular collectings made between 1990 and 2003 on ornamental trees and shrubs in Hungary is given. The second part of the species was collected from fruit trees and shrubs, the third part on herbaceous plants. A total of 33 aphid species was found. Myzocallis (subgen. Lineomyzocallis) walshii (Monell, 1879) from Quercus rubra and Therioaphis tenera (Aizenberg, 1956) from Caragana arborescens are new species for the Hungarian fauna.
Reconsideration on the Phylogenetic Position of Epiclintes (Ciliophora, Stichotrichia) Based on SSrRNA Gene Sequence and Morphogenetic Data

So far, no molecular investigations have been carried out on the systematically uncertain ciliate Epiclintes in spite of the recent reviews. In an attempt to solve this problem, we sequenced the small subunit ribosomal RNA gene of two forms of Epiclintes: E. auricularis auricularis and E. auricularis rarisetus. Phylogenetic trees were then constructed by means of bayesian inference (BI), maximum-likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ) methods in order to test previously presumed phylogenetic assignments of Epiclintes based on morphological and morphogenetic data. The main results are that the two isolates form a branch that is peripheral to all other typical stichotrichs. Epiclintes branched off first in all analyses performed with high BI and moderate MP supporting value (100% BI, 58% MP) while low ML and NJ supporting value (＜50%). This suggests that this genus could represent a unique taxon considering its systematic position. Morphological and ontogenetic investigations on Epiclintes auricularis indicates that this genus demonstrates several special features compared with most other related urostylids: (1) several (instead of one) left-most frontal cirri are developed from the FVT anlage I in E. auricularis rarisetus; (2) buccal and frontoterminal (or migratory) cirri are lacking at interphase and never occur during divisional processes; (3) each FVT anlage, except the anlage I, develops a transverse cirrus; and (4) anlagen for both marginal rows and dorsal kineties are formed de novo. Based on both morphological/morphogenetical and molecular data available, Epiclintes might represent an individual taxon at suborder level, i.e., Epiclintina Wicklow, 1983 (nom. nud.) and as a peripheral branch within stichotrichs s. str.