Miracle-dz/UniFAR-FTUs huggingface dataset:
Cavities and Atomic Packing in Protein Structures and Interfaces

A comparative analysis of cavities enclosed in a tertiary structure of proteins and interfaces formed by the interaction of two protein subunits in obligate and non-obligate categories (represented by homodimeric molecules and heterocomplexes, respectively) is presented. The total volume of cavities increases with the size of the protein (or the interface), though the exact relationship may vary in different cases. Likewise, for individual cavities also there is quantitative dependence of the volume on the number of atoms (or residues) lining the cavity. The larger cavities tend to be less spherical, solvated, and the interfaces are enriched in these. On average 15 Å3 of cavity volume is found to accommodate single water, with another 40–45 Å3 needed for each additional solvent molecule. Polar atoms/residues have a higher propensity to line solvated cavities. Relative to the frequency of occurrence in the whole structure (or interface), residues in β-strands are found more often lining the cavities, and those in turn and loop the least. Any depression in one chain not complemented by a protrusion in the other results in a cavity in the protein–protein interface. Through the use of the Voronoi volume, the packing of residues involved in protein–protein interaction has been compared to that in the protein interior. For a comparable number of atoms the interface has about twice the number of cavities relative to the tertiary structure.
Early features of acute-on-chronic alcoholic liver failure: a prospective cohort study

Background ‘Acute-on-chronic liver failure’ (ACLF) is characterised in a more advanced stage by liver failure associated with multiple other end-organ failure. The global clinical characteristics of this entity remain, however, ill-defined. Objective To characterise and evaluate the clinicopathological features of patients with ACLF compared with patients with chronic decompensated cirrhosis (CHD) in a prospective, homogeneous cohort of patients with histologically proven alcoholic cirrhosis from 2002 to 2007. Results In total 250 patients were screened (ACLF (n=70, 28%) and CHD (n=180, 72%)). Alcoholic liver disease was observed in respectively 61/70 (87%) of patients with ACLF and 72/180 (40%) of patients with CHD. After exclusion of 31 patients, 102 patients were studied: 54 with ACLF (median age 51 years; Child–Pugh 12±2; in-hospital mortality 46% (25/54)) and 48 patients with CHD (median age 53 years; Child–Pugh 10±2; in-hospital mortality 10% (5/48)). In the patients with ACLF who survived the hospital stay, the difference in transplant-free survival compared with patients with CHD tended to attenuate with time. At admission the apparent infection of patient groups was comparable but during hospitalisation infection occurred more frequently in patients with ACLF (31/53 (58%)) than in those with CHD (12/47=26%) (p=0.007). Early signs of infection, positive systemic inflammatory response syndrome (SIRS) criteria at admission and ductular bilirubinostasis (p=0.04), were early features that predicted outcome in ACLF. Conclusion Patients with ACLF have a high short-term mortality but those who survived the acute exacerbation show a long-term outcome comparable to that of patients with CHD. Infection is the most common cause of mortality in these patients. Positive SIRS criteria and ductular bilirubinostasis are early markers of ACLF and might allow more rapid identification of high-risk patients.
Using Digital Elevation Models Derived from Airborne LiDAR and Other Remote Sensing Data to Model Channel Networks and Estimate Fluvial Geomorphological Metrics

Recent advances in remote-sensing technologies and analysis methods, specifically airborne-LiDAR elevation data and corresponding geographical information system (GIS) tools, present new opportunities for automated and rapid fluvial geomorphic (FGM) assessments that can cover entire watersheds. In this thesis, semi-automated GIS tools are used to extract channel centerlines and bankfull width values from digital elevation models (DEM) for five New England watersheds. For each study site, four centerlines are mapped. LiDAR and NED lines are delineated using ArcGIS spatial analyst tools with high-resolution (1-m to 2-m) LiDAR DEMs or USGS National Elevation Dataset (NED) DEMs, respectively. Resampled LiDAR decreases LiDAR DEM resolution and then runs spatial analyst tools. National Hydrography Dataset (NHD) lines are mapped by the USGS. All mapped lines are compared to centerlines delineated from photography and LiDAR DEMs. Bankfull widths at each site are determined through three methods. Regional regression equations are applied using variables derived from LiDAR and NED DEMs separately, producing two sets of width results. Additionally, the Hydrogeomorphological Geoprocessing Toolset (HGM) is used to extract widths from LiDAR data. Widths are also estimated visually from aerial photos and LiDAR DEMs. Widths measured directly in the field or derived from field-data are used as a baseline for comparison. iv I find that with a minimal amount of preprocessing, specifically through DEM resampling, LiDAR data can be used to model a channel that is highly correlated with the shape and location of the mapped channel. NED-derived channels model the mapped channel shape with even greater accuracy, and model the channel location only minimally less accurately. No tool used in this study accurately extracted bankfull width values, but analysis of LiDAR data by the HGM toolset did capture details that could not be resolved using regression equations. Overall, I conclude that automated, computerized LiDAR interpretation needs to improve significantly for the expense of data collection to be cost-effective at a watershed scale.
Cytokine profile in first-episode psychosis, unaffected siblings and community-based controls: the effects of familial liability and childhood maltreatment

Abstract Background Inflammation is a possible biological mechanism underlying the association between childhood maltreatment and psychosis. Previous investigations on this regard were mainly conducted on chronic schizophrenia and lacked control for confounders. We aim to investigate the role of familial liability, childhood maltreatment and recent stress in determining cytokine abnormalities at the onset of psychosis. Methods We recruited 114 first-episode psychosis (FEP) patients, 57 unaffected biological siblings of FEP patients, and 251 community-based controls. Plasma cytokines (IL-1β, IL-6, TNF-α, IFN-γ, IL-4, IL-10 and TGF-β) were measured and differences across the groups analysed after adjusting for potential confounders. Results FEP had a higher pro- and anti-inflammatory cytokine profile (IL-1β, IL-6, TNF-α, IL-10 and TGF-β), which was not observed in unaffected siblings. Siblings presented decreased IL-1β when compared with patients and controls. Childhood maltreatment was associated with higher levels of TGF-β in both patients and siblings when compared with controls. Physical childhood abuse was associated with increased levels of TGF-β in FEP patients but with decreased levels in controls. Other childhood maltreatment subtypes or recent stressors did not affect cytokine levels in any of the groups. Conclusions Normal or reduced cytokines in siblings represent possibly a protective factor and suggest that the identified inflammatory profile in FEP can be a real pathophysiological component of psychosis. Experience of childhood maltreatment may contribute as long-term immune priming for the TGF-β pathway, and increased levels of this cytokine in both patients and siblings exposed to childhood maltreatment point to a possible biological candidate of familial risk for psychosis.
Heterochronic shifts mediate ecomorphological convergence in skull shape of microcephalic sea snakes.

Morphological variation among the true sea snakes (Hydrophiinae), a clade of fully aquatic elapid snakes, includes an extreme 'microcephalic' ecomorph that has a very small head atop a narrow forebody, while the hind body is much thicker (up to 3 times the forebody girth). Previous research has demonstrated that this morphology has evolved at least nine times as a consequence of dietary specialization on burrowing eels, and has also examined morphological changes to the vertebral column underlying this body shape. The question addressed in this study is what happens to the skull during this extreme evolutionary change? Here we use X-ray micro-computed tomography and geometric morphometric methods to characterize cranial shape variation in 30 species of sea snakes. We investigate ontogenetic and evolutionary patterns of cranial shape diversity to understand whether cranial shape is predicted by dietary specialization, and examine whether cranial shape of microcephalic species may be a result of heterochronic processes. We show that the diminutive cranial size of microcephalic species has a convergent shape that is correlated with trophic specialization to burrowing prey. Furthermore, their cranial shape is predictable for their size and very similar to that of juvenile individuals of closely related but non-microcephalic sea snakes. Our findings suggest that heterochronic changes (resulting in paedomorphosis) have driven cranial shape convergence in response to dietary specializations in sea snakes.
Effect of protein cryoconcentration and processing conditions on kinetics of dimer formation for a monoclonal antibody: A case study on bioprocessing

Monoclonal antibodies (mAbs) may be prone to self‐association leading to formation of dimers, trimers, or other high molecular weight species during bio‐processing. In order to implement appropriate manufacturing control strategies during bio‐processing, it is important to understand various real life bio‐processing conditions where such self‐associations may manifest. One such case study is presented here of increase in dimer content for an mAb during scale‐up bio‐processing and the approach taken to understand the under‐lying mechanism. In this example, a therapeutic mAb demonstrated a consistently higher dimer values (~0.5% higher) in the drug product (DP) during release when compared to the same value measured in the corresponding drug substance (DS) lot. This observation was interesting since the DS was supplied frozen, and the DS and DP share the same formulation composition and therefore investigation of this dimer change was the scope of the characterization study. Variable path length spectroscopy and size exclusion chromatography was used for protein quantification and to monitor %dimer respectively during characterization of fill‐finish unit operations. At the start of DP manufacturing process, immediately after thaw of bulk DS, a protein concentration gradient was observed and the concentration ranged from 90 mg/mL (top of container) to 210 mg/mL (bottom of container). The dimerization kinetics in the same DS container was dependent on concentration with higher concentrations demonstrating higher rates of dimerization. After the bulk DS was mixed for further processing, %dimer in purified bulk DS was quantitated to be approximately 1.4% which is identical to levels observed during scale‐up manufacturing of DP. After each unit operation, the in‐process samples tested for %dimer showed a gradual increase in dimer as a function of time over the next 7 days accumulating to 1.8% dimer at the end of DP manufacturing process. Samples subjected to static incubation at 2–8°C and room temperature (RT; 15–25°C) showed a gradual increase in dimer over the same time frame; however, the rate of increase in dimer at RT was higher compared to samples stored at 2–8°C. The results from this demonstrate two important key findings: self‐association kinetics of mAbs could be exacerbated by protein cryoconcentration and temperature conditions during bioprocessing. Since these two parameters are commonly encountered during manufacturing, the proposed mitigation strategy is to ensure homogeneity of the bulk DP during processing. The temperature dependent self‐association kinetics of mAb could be mitigated by processing at lower temperature (e.g., 2–8°C) and by storing the finished DP at lower temperature after manufacturing. The results from this study also highlight the criticality of setting slightly wider specifications for DP compared to DS following ICH Q6B guidelines.
Systematic Review of Patient-Derived Xenograft Models for Preclinical Studies of Anti-Cancer Drugs in Solid Tumors

Patient-derived xenograft (PDX) models are used as powerful tools for understanding cancer biology in PDX clinical trials and co-clinical trials. In this systematic review, we focus on PDX clinical trials or co-clinical trials for drug development in solid tumors and summarize the utility of PDX models in the development of anti-cancer drugs, as well as the challenges involved in this approach, following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Recently, the assessment of drug efficacy by PDX clinical and co-clinical trials has become an important method. PDX clinical trials can be used for the development of anti-cancer drugs before clinical trials, with their efficacy assessed by the modified response evaluation criteria in solid tumors (mRECIST). A few dozen cases of PDX models have completed enrollment, and the efficacy of the drugs is assessed by 1 × 1 × 1 or 3 × 1 × 1 approaches in the PDX clinical trials. Furthermore, co-clinical trials can be used for personalized care or precision medicine with the evaluation of a new drug or a novel combination. Several PDX models from patients in clinical trials have been used to assess the efficacy of individual drugs or drug combinations in co-clinical trials.
Semantic Web and semantic Web services: father and son or indivisible twins?

The semantic Web is, without a doubt, gaining momentum in both industry and academia. The recent International Semantic Web Conference (ISWC) attracted more than 500 researchers; major vendors including IBM, Oracle, and Software AG have released or announced products; and the forthcoming Semantic Technology Conference in San Jose, California, is poised to be an impressive showcase for executives and venture capitalists on the business potential of semantic technologies. Unfortunately, semantic Web services are underrepresented on the agenda, at least if we take the number of scientific publications about semantic Web services as a proxy. Most semantic Web researchers dedicate their attention to annotating Web content stored in static documents or database-driven applications. Semantic Web services (SWS) frameworks are mandatory components of the semantic Web, primarily because entities are more willing to expose functionality than data in business settings.
The Use of Pedicle-Screw Internal Fixation for the Operative Treatment of Spinal Disorders*

Pedicle screws have dramatically improved the outcomes of spinal reconstruction requiring spinal fusion. Short-segment surgical treatments based on the use of pedicle screws for the treatment of neoplastic, developmental, congenital, traumatic, and degenerative conditions have been proved to be practical, safe, and effective. The Funnel Technique provides a straightforward, direct, and inexpensive way to very safely apply pedicle screws in the cervical, thoracic, or lumbar spine. Carefully applied pedicle-screw fixation does not produce severe or frequent complications. Pedicle-screw fixation can be effectively and safely used wherever a vertebral pedicle can accommodate a pedicle screw--that is, in the cervical, thoracic, or lumbar spine. Training in pedicle-screw application should be standard in orthopaedic training programs since pedicle-screw fixation represents the so-called gold standard of spinal internal fixation.
Global Regulator PhoP is Necessary for Motility, Biofilm Formation, Exoenzyme Production, and Virulence of Xanthomonas citri Subsp. citri on Citrus Plants

Citrus canker caused by Xanthomonas citri subsp. citri is one of the most important bacterial diseases of citrus, impacting both plant growth and fruit quality. Identifying and elucidating the roles of genes associated with pathogenesis has aided our understanding of the molecular basis of citrus-bacteria interactions. However, the complex virulence mechanisms of X. citri subsp. citri are still not well understood. In this study, we characterized the role of PhoP in X. citri subsp. citri using a phoP deletion mutant, ΔphoP. Compared with wild-type strain XHG3, ΔphoP showed reduced motility, biofilm formation, as well as decreased production of cellulase, amylase, and polygalacturonase. In addition, the virulence of ΔphoP on citrus leaves was significantly decreased. To further understand the virulence mechanisms of X. citri subsp. citri, high-throughput RNA sequencing technology (RNA-Seq) was used to compare the transcriptomes of the wild-type and mutant strains. Analysis revealed 1017 differentially-expressed genes (DEGs), of which 614 were up-regulated and 403 were down-regulated in ΔphoP. Gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses suggested that the DEGs were enriched in flagellar assembly, two-component systems, histidine metabolism, bacterial chemotaxis, ABC transporters, and bacterial secretion systems. Our results showed that PhoP activates the expression of a large set of virulence genes, including 22 type III secretion system genes and 15 type III secretion system effector genes, as well as several genes involved in chemotaxis, and flagellar and histidine biosynthesis. Two-step reverse-transcription polymerase chain reaction analysis targeting 17 genes was used to validate the RNA-seq data, and confirmed that the expression of all 17 genes, except for that of virB1, decreased significantly. Our results suggest that PhoP interacts with a global signaling network to co-ordinate the expression of multiple virulence factors involved in modification and adaption to the host environment during infection.
Extracellular membrane vesicles harbouring viral genomes.

Cells from the three domains of life produce extracellular membrane vesicles (MVs), suggesting that MV production is a fundamental aspect of cellular physiology. We have recently shown that MVs produced by the hyperthermophilic archaeon Thermococcus kodakaraensis can be used as vehicles to transfer exogenous recombinant plasmid DNA from cell to cell. Here, we show that Thermococcus nautilus, which harbours three plasmids, pTN1, pTN2 and pTN3, produces MVs, and that some of them selectively incorporate pTN1 and pTN3. Interestingly, pTN3 represents the genome of a defective virus, which encodes signature proteins common to a large group of viruses infecting hosts from all three cellular domains. However, preparations of MVs produced by T. nautilus have a protein composition similar to that of classical MVs from Thermococcales and do not contain the viral major capsid protein encoded by pTN3. Our results suggest that MVs can serve as vehicles for the intercellular transport of viral genomes and facilitate recombination between viral, plasmid and/or cellular chromosomes in the absence of viral infection.
Arnold‐Chiari type 1 malformation in Potocki–Lupski syndrome

Potocki–Lupski syndrome (PTLS) is a genetic disorder that results from an interstitial duplication within chromosome 17p11.2. Children with PTLS typically present with infantile hypotonia, failure to thrive, and global developmental delay with or without major organ system involvement. Systematic clinical studies regarding growth, cardiovascular disease, and neurocognitive profiles have been published; however, systematic evaluation of central nervous system structure by magnetic resonance imaging (MRI) of the brain has not been reported. Herein, we describe three patients with PTLS who were found—in the course of routine clinical care—to have a type 1 Arnold‐Chiari malformation (CM‐1). This finding raises the question of whether the incidence of CM‐1 is increased in PTLS, and hence, if an MRI of the brain should be considered in the evaluation of all patients with this chromosomal duplication syndrome.
Recent progress in nanotechnology-based novel drug delivery systems in designing of cisplatin for cancer therapy: an overview

Abstract Cisplatin cis-(diammine)dichloridoplatinum(II) (CDDP) is the first platinum-based complex approved by the food and drug administration (FDA) of the United States (US). Cisplatin is the first line chemotherapeutic agent used alone or combined with radiations or other anti-cancer agents for a broad range of cancers such as lung, head and neck. Aroplatin™, Lipoplatin™ and SPI-077 are PEGylated liposome-based nano-formulations that are still under clinical trials. They have many limitations, for example, poor aqueous solubility, drug resistance and toxicities, which can be overcome by encapsulating the cisplatin in Nemours nanocarriers. The extensive literature from different electronic databases covers the different nano-delivery systems that are developed for cisplatin. This review critically emphasizes on the recent advancement, development, innovations and updated literature reported for different carrier systems for CDDP.
Illumination invariant object tracking based on multiscale phase

Illumination change usually results in challenging problems for many computer vision applications such as recognition, tracking and motion analysis. In this paper, an illumination invariant object tracking approach is proposed. Video feature information is captured using a monogenic scale space representation. From this representation, multiscale phase information, which has the advantage of being invariant to illumination change, can be extracted. By minimizing an energy function, multiscale phase information between frames are matched. Based on the matched phase information, moving objects under high illumination variation can be successfully tracked. Experimental results show that the presented approach is robust to illumination change. As a comparison, we also demonstrate the tracking results from the mean shift tracker, it is proved that our approach outperforms the mean shift tracker under the high lighting change environment.
Enhanced stability of immobilized keratinolytic protease on electrospun nanofibers

Abstract Feathers from poultry industries are considered a major pollutant and its degradation is a challenging problem due to its recalcitrant nature. The high cost of energy and loss of essential amino acids by conventional methods have paved a way for an environmentally benign approach using microbial keratinolytic proteases. The widespread application of keratinolytic proteases is limited due to autolysis and denaturation of the enzyme upon storage. Immobilization overcomes these disadvantages by adsorbing the enzyme onto a solid support. Recently, electrospun nanofibers have been used due to their increased surface area and porous structure. The biocompatible and hydrophilic polyvinyl alcohol (PVA) has been blended with biodegradable chitosan for immobilization in electrospinning. The present study focuses on feather degradation by immobilized keratinolytic proteases on electrospun nanofibers. The keratinolytic protease production was enhanced by using a media containing hydrolyzed feather under optimized conditions. The immobilized keratinolytic protease on electrospun PVA chitosan (PVA-Ch) nanofibers (100–150 nm diameter) degraded the chicken feathers with 88% efficiency at the end of 72 hr.