Miracle-dz/UniFAR-FTUs huggingface dataset:
Harnessing Fc/FcRn Affinity Data from Patents with Different Machine Learning Methods

Monoclonal antibodies are biopharmaceuticals with a very long half-life due to the binding of their Fc portion to the neonatal receptor (FcRn), a pharmacokinetic property that can be further improved through engineering of the Fc portion, as demonstrated by the approval of several new drugs. Many Fc variants with increased binding to FcRn have been found using different methods, such as structure-guided design, random mutagenesis, or a combination of both, and are described in the literature as well as in patents. Our hypothesis is that this material could be subjected to a machine learning approach in order to generate new variants with similar properties. We therefore compiled 1323 Fc variants affecting the affinity for FcRn, which were disclosed in twenty patents. These data were used to train several algorithms, with two different models, in order to predict the affinity for FcRn of new randomly generated Fc variants. To determine which algorithm was the most robust, we first assessed the correlation between measured and predicted affinity in a 10-fold cross-validation test. We then generated variants by in silico random mutagenesis and compared the prediction made by the different algorithms. As a final validation, we produced variants, not described in any patents, and compared the predicted affinity with the experimental binding affinities measured by surface plasmon resonance (SPR). The best mean absolute error (MAE) between predicted and experimental values was obtained with a support vector regressor (SVR) using six features and trained on 1251 examples. With this setting, the error on the log(KD) was less than 0.17. The obtained results show that such an approach could be used to find new variants with better half-life properties that are different from those already extensively used in therapeutic antibody development.
Adaptive Polynomials Local Refinement for Resolving Flame Structure

A thin diffusive flame structure in an asymptotic form is resolved by the local polynomial refinement approach using the Gauss-Lobatto formulation. The continuity condition at the grid block interface must be enforced for the diffusion dominant equation. A multiple-point, unequal spaced, differencing approximation to preserve the spectral accurate and to increase computationally efficient is implemented. It is found that the shared first and second derivatives at the gird block interface can be computed from the roots of polynomials of adjacent blocks and effectively retains the numerical resolution in comparison with the L2 norm projection, recovery-based, penalty, and reconstruction methods in applications. The computed flame thickness agrees well with results using a systematic mesh refinement approach.
Direct Detection of KPC Peak from Positive Blood Cultures Using MALDI-TOF MS: Are We There Yet?

Detecting carbapenemase-associated carbapenem resistance is a subject of major clinical and epidemiological concern as it influences therapeutic choice. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed as a means to assess bacterial resistance mechanisms. We aimed to detect the KPC enzyme directly from positive blood cultures using MALDI-TOF MS. To do so, 102 clinical Enterobacteria were evaluated, including 59 blaKPC positives. Proteins were extracted using formic acid, isopropyl alcohol, and water (17:33:50) and spotted onto a steel target plate using the double-layer sinapinic acid technique. Two parameters were considered: (i) the visual detection of a clear peak with the expected KPC m/z and (ii) the evaluation of the relative intensity of the ions in the peak. A peak was observed in 56/59 blaKPC-positive isolates (94.9% sensitivity), with no false-positive results (100% specificity). When considering intensity, with a cut-off ≥120 (a.u.), sensitivity was 94.9% and specificity was 95.3%. We proposed a “buffer” zone, with intermediate values of intensity (115 to 125) reaching 100% sensitivity and specificity. The detection of KPC peaks directly from positive blood cultures using MALDI-TOF MS is feasible and rapid, which may improve appropriate patient therapy and antimicrobial stewardship.
Identification of major QTLs for yield-related traits with improved genetic map in wheat

Introduction Identification of stable major quantitative trait loci (QTLs) for yield-related traits is important for yield potential improvement in wheat breeding. Methods In the present study, we genotyped a recombinant inbred line (RIL) population using the Wheat 660K SNP array and constructed a high-density genetic map. The genetic map showed high collinearity with the wheat genome assembly. Fourteen yield-related traits were evaluated in six environments for QTL analysis. Results and Discussion A total of 12 environmentally stable QTLs were identified in at least three environments, explaining up to 34.7% of the phenotypic variation. Of these, QTkw-1B.2 for thousand kernel weight (TKW), QPh-2D.1 (QSl-2D.2/QScn-2D.1) for plant height (PH), spike length (SL) and spikelet compactness (SCN), QPh-4B.1 for PH, and QTss-7A.3 for total spikelet number per spike (TSS) were detected in at least five environments. A set of Kompetitive Allele Specific PCR (KASP) markers were converted based on the above QTLs and used to genotype a diversity panel comprising of 190 wheat accessions across four growing seasons. QPh-2D.1 (QSl-2D.2/QScn-2D.1), QPh-4B.1 and QTss-7A.3 were successfully validated. Compared with previous studies, QTkw-1B.2 and QPh-4B.1 should be novel QTLs. These results provided a solid foundation for further positional cloning and marker-assisted selection of the targeted QTLs in wheat breeding programs.
Discrete PSO with GA Operators for Document

The paper presents Discrete PSO algorithm for document clustering problems. This algorithm is hybrid of PSO with GA operators. The proposed system is based on population-based heuristic search technique, which can be used to solve combinatorial optimization problems, modeled on the concepts of cultural and social rules derived from the analysis of the swarm intelligence (PSO) with GA operators such as crossover and mutation. In standard PSO the non-oscillatory route can quickly cause a particle to stagnate and also it may prematurely converge on suboptimal solutions that are not even guaranteed to local optimal solution. In this paper a modification strategy is proposed for the particle swarm optimization (PSO) algorithm and applied in the document corpus. The strategy adds reproduction by using crossover and mutation operators when the stagnation in movement of the particle is identified. Reproduction has the capability to achieve faster convergence and better solution. Experiments results are examined with document corpus. It demonstrates that the proposed DPSO algorithm statistically outperforms the Simple PSO.
A Five-Year Update on Matrix Compounds for MALDI-MS Analysis of Lipids

Matrix-assisted laser desorption and ionization (MALDI) is a widely used soft-ionization technique of modern mass spectrometry (MS). MALDI enables the analysis of nearly all chemical compounds—including polar and apolar (phospho)lipids—with a minimum extent of fragmentation. MALDI has some particular advantages (such as the possibility to acquire spatially-resolved spectra) and is competitive with the simultaneously developed ESI (electrospray ionization) MS. Although there are still some methodological aspects that need to be elucidated in more detail, it is obvious that the careful selection of an appropriate matrix plays the most important role in (lipid) analysis. Some lipid classes can be detected exclusively if the optimum matrix is used, and the matrix determines the sensitivity by which a particular lipid is detected within a mixture. Since the matrix is, thus, crucial for optimum results, we provide here an update on the progress in the field since our original review in this journal in 2018. Thus, only the development during the last five years is considered, and lipids are sorted according to increasing complexity, starting with free fatty acids and ending with cardiolipins and phosphoinositides.
A Study Protocol on the Effectiveness of Radial Shockwave Therapy on Myofascial Pain Syndrome: A Mixed Methods Study That Combines a Randomised Control Trial and Semi-Structured Interviews

Background: Myofascial pain syndrome (MPS) is a common, costly and often persistent musculoskeletal problem. Radial shockwave (RSW) is one of the most common treatments for MFS. However, there is very low-level evidence to support its short-term benefit, due to poor methodological qualities. Furthermore, previous studies have not considered the experiences of patients regarding this intervention. This study will investigate the effectiveness of RSW compared to a sham (placebo) for patients with MPS and establish the experiences of patients receiving the treatment. Methods: A mixed methods study of a pragmatic randomised controlled trial and semi-structured-interviews that will involve 120 potential participants with MPS is used. The intervention group will receive six sessions of RSW: 1.5 bars, 2000 pulses, frequency 15 Hz. The control group will receive an identical treatment except that they will receive a no-energy shock of 0.3 bar. Results: The outcome measures are a numeric pain scale, neck disability index (NDI), pressure pain threshold (PPT) and SF-12 questionnaires at 4 and 8 weeks’ follow-up between the two groups. Conclusion: The expectation is that this study will add to the body of knowledge required to make effective treatment choices on RSW in the management MFS.
Improvement of a Pound-Drever-Hall Technique to Measure Precisely the Free Spectral Range of a Fabry-Perot Etalon

We examine the principle of a modified Pound-Drever-Hall (PDH) technique to measure the free spectral range of a Fabry-Perot etalon (FPE). The FPE's periodic transmission of phase-modulated light allows us to adopt a sampling theorem to develop a new relationship for the PDH error signal. This leads us to find the key parameters governing the measurement accuracy: the phase modulation index ${\beta}$ and the FPE finesse. Without any additional complexity for background noise reduction, we achieve a measurement accuracy of 0.5 ppm. The improvement is mainly attributed to the wide-band phase modulation approaching ${\beta}=10$ , and partly to the use of both reflected and transmitted light from the FPE and good FPE finesse.
Methods for matching English language addresses

Addresses occupy a niche location within the landscape of textual data, due to the positional importance carried by every word, and the geographic scope it refers to. The task of matching addresses happens every day and is present in various fields such as mail redirection, entity resolution, etc. Our work defines, and formalizes a framework to generate matching and mismatching pairs of addresses in the English language, and use it to evaluate various methods to automatically perform address matching. These methods vary widely from distance‐based approaches to deep learning models. By studying the Precision, Recall, and Accuracy metrics of these approaches, we obtain an understanding of the best suited method for this setting of the address matching task.
High Expression of COA6 Is Related to Unfavorable Prognosis and Enhanced Oxidative Phosphorylation in Lung Adenocarcinoma

Mitochondrial metabolism plays an important role in the occurrence and development of cancers. Cytochrome C oxidase assembly factor six (COA6) is essential in mitochondrial metabolism. However, the role of COA6 in lung adenocarcinoma (LUAD) remains unknown. Here we report that the expression of COA6 mRNA and protein were upregulated in LUAD tissues compared with lung normal tissues. We found that COA6 had high sensitivity and specificity to distinguish LUAD tissues from normal lung tissues shown by a receiver operating characteristic (ROC) curve. In addition, our univariate and multivariate Cox regression analysis indicated that COA6 was an independent unfavorable prognostic factor for LUAD patients. Furthermore, our survival analysis and nomogram showed that a high expression of COA6 mRNA was related to the short overall survival (OS) of LUAD patients. Notably, our weighted correlation network analysis (WGCNA) and functional enrichment analysis revealed that COA6 may participate in the development of LUAD by affecting mitochondrial oxidative phosphorylation (OXPHOS). Importantly, we demonstrated that depletion of COA6 could decrease the mitochondrial membrane potential (MMP), nicotinamide adenine dinucleotide (NAD) + hydrogen (H) (NADH), and adenosine triphosphate (ATP) production in LUAD cells (A549 and H1975), hence inhibiting the proliferation of these cells in vitro. Together, our study strongly suggests that COA6 is significantly associated with the prognosis and OXPHOS in LUAD. Hence, COA6 is highly likely a novel prognostic biomarker and therapeutic target of LUAD.
An Ultrawideband Compact Magneto-Electric Dipole Antenna and Its Coupled Array

A novel magneto-electric dipole antenna with compact structure and unidirectional radiation is proposed. The electrical connection between the U-shaped floor and the electric dipole (E-dipole) was cutoff to reduce the profile height, and the straight-line edges of the original dipoles were replaced with an arc-shaped one to stabilize the voltage standing wave ratio (VSWR). Furthermore, when the antenna element is employed as the coupled array unit, the altering of the element number and the way the array is assembled has no significant impact on the radiation performance, which is almost the same as that of a single antenna. The modified prototype of a 2 × 2 array with the dimension of 0. 33λL × 0. 28λL × 0. 10λL is fabricated and measured. Results indicate that the antenna array exhibits a band ratio of 30.9 with VSWR ≤ 2.3 in 98 MHz–3.03 GHz, realized gain of 4.1–14.9 dBi and unidirectional pattern with SLL < −10 dB from 98 to 700 MHz.
Optical Coherence Tomography in Glaucoma

O ptical coherence tomography (OCT), a noninva-sive imaging modality that uses low-coherence light to obtain a high-resolution cross-section of biological structures, is changing the field of ophthalmology. The technology has evolved dramatically since its first description by Huang et al in 1991. 1 The most significant leap forward occurred when the moving reference mirror used during the collection of time-domain (TD) OCT data was abandoned in favor of Fourier analysis of collected data. As a result, the current spectral-domain (SD) OCT technology collects up to 55,000 A-scans per second with an axial resolution of 5 µm—a 100-fold improvement over the earlier-generation TD-OCT. 2 Obtaining large data cubes quickly reduces test-retest variability, allows three-dimensional reconstruction and alignment, improves registration, and facilitates test-retest comparisons. Not surprisingly, SD-OCT has been shown to have better diagnostic ability for glaucoma and its progression than TD-OCT. 3 CURRENT CHALLENGES IN GLAUCOMA MANAGEMENT The lack of objective structural or functional tests proven to detect early disease and progression makes glaucoma difficult to manage. As with perimetric findings , structural progression may be focal or diffuse, and it may occur well before any visual deficits are apparent. Structural tests traditionally relied on clinicians' recognizing changes to the optic disc and retinal nerve fiber layer (RNFL) on clinical examination. 4 Given that the nerve anatomy and topography demonstrate significant inter-individual variability, clinicians frequently find it difficult to distinguish physiologic variants such as cupping from those caused by glaucoma (neuroretinal rim loss). Large studies have also demonstrated disagreements between structural and functional tests. Practitioners rely heavily on clinical experience, and SD-OCT offers objectivity by providing a quantitative assessment of the inner retina. 8 PERIPAPILLARY RNFL EVALUATION Peripapillary RNFL thickness, as measured by SD-OCT, is the most common method for identifying and monitoring structural damage in glaucoma. 9 This modality detects early, preperimetric disease and progression in glaucoma suspects (Figure). 10 Formulas that approximate the amount of retinal ganglion cell (RGC) loss, a hallmark of glaucomatous damage, from OCT RNFL measurements have also been derived, as have methods of combining both structure and function. EVALUATION OF MACULAR THICKNESS The macula is densely populated by RGCs, containing 30% of the total number of these cells while occupying only 2% of the retina's area. Zeimer et al hypothesized that the loss of RGCs in early glaucoma is more likely to occur in the macula. An essential imaging modality for diagnosis, monitoring, and management …
Evolutionary history and patterns of divergence in three tropical east Asian squirrels across the Isthmus of Kra

Understanding the biotic and abiotic mechanisms underlying the generation and maintenance of biogeographic transitions represent long‐standing topics in evolutionary biology. The Isthmus of Kra (IOK) divides Sundaland and Indochina and constitutes a poorly characterized terrestrial biogeographic transition. Here we looked at population genetic structure of three species that are distributed across the IOK to gain insights into the drivers that have shaped this transition and regional diversification patterns.
Aspergillus luchuensis, an Endophyte Fungus from the Metal Hyperaccumulator Plant Prosopis laevigata, Promotes Its Growth and Increases Metal Translocation

Heavy metal pollution is a worldwide environmental and human health problem. Prosopis laevigata is a hyperaccumulator legume that bioaccumulates Pb, Cu and Zn. With interest in designing phytoremediation strategies for sites contaminated with heavy metals, we isolated and characterized endophytic fungi from the roots of P. laevigata growing on mine tailings located in Morelos, Mexico. Ten endophytic isolates were selected by morphological discrimination and a preliminary minimum inhibitory concentration was determined for zinc, lead and copper. A novel strain of Aspergillus closest to Aspergillus luchuensis was determined to be a metallophile and presented a marked tolerance to high concentrations of Cu, Zn and Pb, so it was further investigated for removal of metals and promotion of plant growth under greenhouse conditions. The control substrate with fungi promoted larger size characters in P. laevigata individuals in comparison with the other treatments, demonstrating that A. luchuensis strain C7 is a growth-promoting agent for P. laevigata individuals. The fungus favors the translocation of metals from roots to leaves in P. laevigata, promoting an increased Cu translocation. This new A. luchuensis strain showed endophytic character and plant growth-promotion activity, high metal tolerance, and an ability to increase copper translocation. We propose it as a novel, effective and sustainable bioremediation strategy for copper-polluted soils.
Ketoprofen-Based Polymer-Drug Nanoparticles Provide Anti-Inflammatory Properties to HA/Collagen Hydrogels

Current limitations of wound dressings for treating chronic wounds require the development of novel approaches. One of these is the immune-centered approach, which aims to restore the pro-regenerative and anti-inflammatory properties of macrophages. Under inflammatory conditions, ketoprofen nanoparticles (KT NPs) can reduce pro-inflammatory markers of macrophages and increase anti-inflammatory cytokines. To assess their suitability as part of wound dressings, these NPs were combined with hyaluronan (HA)/collagen-based hydro- (HGs) and cryogels (CGs). Different HA and NP concentrations and loading techniques for NP incorporation were used. The NP release, gel morphology, and mechanical properties were studied. Generally, colonialization of the gels with macrophages resulted in high cell viability and proliferation. Furthermore, direct contact of the NPs to the cells reduced the level of nitric oxide (NO). The formation of multinucleated cells on the gels was low and further decreased by the NPs. For the HGs that produced the highest reduction in NO, extended ELISA studies showed reduced levels of the pro-inflammatory markers PGE2, IL-12 p40, TNF-α, and IL-6. Thus, HA/collagen-based gels containing KT NPs may represent a novel therapeutic approach for treating chronic wounds. Whether effects observed in vitro translate into a favorable profile on skin regeneration in vivo will require rigorous testing.
Transmittance of TiO2 nanoparticle-based films deposited by CO2 laser heating

Nanoelectrospray laser deposition (NELD) of semiconductor and metal nanoparticles is a powerful and potential technology for the on-demand printing of precise and complex functional microarchitectures. In this study, a CO2 laser is used to deposit and sinter titanium dioxide (TiO2) nanoparticles on borosilicate and quartz substrates for transparent film applications. The CO2 laser is chosen for sintering because TiO2 has a lower spectral absorption at 10.6 μm wavelength. Therefore, the 10.6 μm laser can transmit through the deposited TiO2 films, and then, the whole film thickness can be thermally modified by the heating effect of laser. The effects of wet-deposition process parameters and laser processing parameters on the morphological, optical, and structural properties of TiO2 patterns are examined. The TiO2 microstructure and surface morphology were studied by optical and scanning electron microscopy techniques. X-ray diffraction (XRD) was used to investigate the structural characteristics after laser sintering. The optical transmittance of the wet and sintered TiO2 films was characterized by UV/Vis/NIR spectrophotometry. We established that the overall improvement of the morphological and optical properties of the sintered films originates from the enhanced bonding and physical interconnectivity of TiO2 nanoparticles, resulting in the formation of a dense and compact ceramic layer. XRD data points out that the anatase phase of TiO2 is preserved after laser sintering, eliminating the presence of TiO2 rutile traces. An average transmittance above ~90% was achieved in the NIR region.