Miracle-dz/UniFAR-FTUs huggingface dataset:
Overcoming Limitations of Microparticle Measurement by Flow Cytometry

Circulating microparticles are submicron vesicles released from cell membranes in response to activation or apoptosis. Acknowledgment of their role both as markers and pathogenic effectors in thrombosis, inﬂammation, and the spread of cancer has increased the interest of their measurement in clinical practice. However, assessment of their clinical use is impeded by technological issues. Among the different methodologies available, ﬂow cytometry is the most commonly used technique. This review addresses ﬂow cytometry limitations in microparticle measurement that may be subdivided into three domains: sizing, probing, and counting. This article also covers the various standardization strategies and technological improvements that have been proposed to overcome these limitations. New tools using size-calibrated beads and recent progress in instrumentation have opened new avenues to improve detection of microparticle populations of smaller sizes. Signiﬁcant optimization in microparticle detection is also expected from the use of new ﬂuorescent dyes and the establishment of practical recommendations. Finally, absolute counting of microparticles will also beneﬁt from adapted bead-based strategies or, alternatively, from the generalized availability of volumetric systems. Overall, recent technological improvements maintain ﬂow cytometry as a highly competitive analytical method to measure microparticles. Challenging these evolutions in pathological situations is a mandatory step to validate their real impact in clinical practice.
Uterine Receptivity and the Ramifications of Ovarian Stimulation on Endometrial Function

Controlled ovarian stimulation (COS) is widely used in assisted reproduction techniques (ART). However, hormonal treatment induces endometrial alterations that may alter implantation rates compared with natural cycles. Endometrial alterations have been observed by histological and biochemical techniques. The recent developments in functional genomics have provided objective tools to analyze the endometrium in natural cycles and evaluate the impact of COS protocols in endometrial development. This article describes the fundamental aspects of endometrial receptivity in natural cycles and reports how COS affects the morphology, biochemistry, and the genomic pattern of the endometrium.
Snippet Comment Generation Based on Code Context Expansion

Code commenting plays an important role in program comprehension. Automatic comment generation helps improve software maintenance efficiency. The code comments to annotate a method mainly include header comments and snippet comments. The header comment aims to describe the functionality of the entire method, thereby providing a general comment at the beginning of the method. The snippet comment appears at multiple code segments in the body of a method, where a code segment is called a code snippet. Both of them help developers quickly understand code semantics, thereby improving code readability and code maintainability. However, existing automatic comment generation models mainly focus more on header comments because there are public datasets to validate the performance. By contrast, it is challenging to collect datasets for snippet comments because it is difficult to determine their scope. Even worse, code snippets are often too short to capture complete syntax and semantic information. To address this challenge, we propose a novel Snippet Comment Generation approach called SCGen. First, we utilize the context of the code snippet to expand the syntax and semantic information. Specifically, 600,243 snippet code-comment pairs are collected from 959 Java projects. Then, we capture variables from code snippets and extract variable-related statements from the context. After that, we devise an algorithm to parse and traverse abstract syntax tree (AST) information of code snippets and corresponding context. Finally, SCGen generates snippet comments after inputting the source code snippet and corresponding AST information into a sequence-to-sequence-based model. We conducted extensive experiments on the dataset we collected to evaluate our SCGen. Our approach obtains 18.23 in BLEU-4 metrics, 18.83 in METEOR, and 23.65 in ROUGE-L, which outperforms state-of-the-art comment generation models.
Partition Crossover can Linearize Local Optima Lattices of k-bounded Pseudo-Boolean Functions

When Partition Crossover is used to recombine two parents which are local optima, the offspring are all local optima in the smallest hyperplane subspace that contains the two parents. The offspring can also be organized into a non-planar hypercube "lattice. " Furthermore, all of the offspring can be evaluated using a simple linear equation. When a child of Partition Crossover is a local optimum in the full search space, the linear equation exactly determines its evaluation. When a child of Partition Crossover can be improved by local search, the linear equation is an upper bound on the evaluation of the associated local optimum when minimizing. This theoretical result holds for all k-bounded Pseudo-Boolean optimization problems, including MAX-kSAT, QUBO problems, as well as random and adjacent NK landscapes. These linear equations provide a stronger explanation as to why the "Big Valley" distribution of local optima exists. We fully enumerate a sample of NK landscapes to collect frequency information to complement our theoretical results. We also introduce new algorithmic contributions that can 1) expand smaller lattices in order to find larger lattices that contain additional local optima, and 2) introduce an efficient method to find new improving moves in lattices using score vectors.
Modification of an implicit approach based on nonstandard rules for structural dynamics analysis

Abstract The present study aims to modify a recently suggested implicit approach consisted of the approximate Euler method and closed-form exponential mapping (herein referred to as the Liu scheme) for the dynamic analysis of structures. Such modification has been developed based upon nonstandard rules. The equation of motion is formulated in the augmented dynamic space to apply the exponential mapping as a group preserving scheme. The formulation of the proposed method involves the hyperbolic sine and cosine functions. The method is therefore prone to divergence due to the behavior of the hyperbolic functions in structures with a high ratio of stiffness to mass. In the present study, to consider the properties of the structural equation into the formulation of the time step size and thereby avoid the divergence, a parameter, known as stability parameter, is thus derived from the exact solution of the equation of motion based on nonstandard rules. Embedding this parameter into the proposed method improves its stability. Afterward, for evaluating the performance of the proposed method, it is applied to several structures with different loading patterns while implemented in programing environment of the Matlab software. The results are compared to those of several commonly used numerical methods in structural applications. It is found that the proposed method has acceptable convergence and accuracy, and low time consumption compared to several commonly used methods. Furthermore, its stability is guaranteed by embedding the stability parameter into the proposed method.
Bioconvection transport of upper convected Maxwell nanoliquid with gyrotactic microorganism, nonlinear thermal radiation, and chemical reaction

Abstract The microorganisms’ concept has appealed substantial consideration of modern researchers because of its utilization in commercial and industrial products, for illustration, biofuel (prepared from the waste), drug delivery, and fertilizers. Keeping such utilizations of microorganisms in mind, an analysis based on gyrotactic microorganisms featuring the mixed convective nonlinear radiative Maxwell nanoliquid stagnation point flow configured by permeable stretching surface is presented. Boundary layer stretching flow subjected to transpiration effects is formulated. Modeling is based on Buongiorno’s nanoliquid model. This model captures Brownian diffusion along with thermophoresis aspects. Energy expression is formulated under nonlinear version of radiative heat-flux, heat source, thermal Robin conditions, and heat sink. Mass transport analysis is presented considering solutal Robin conditions and chemical reaction. In addition, the Robin conditions for motile microorganisms are also considered. The complex mathematical expressions of Maxwell liquid are simplified utilizing the Boundary layer concept and then suitable transformations assist to obtain the mathematical problems in ordinary differential forms. The analytical approach (that is homotopy analysis methodology) is utilized for computational analysis. The outcomes obtained are presented graphically and numerically. The detailed description of emerging physical non-dimensional parameters is included. Our findings indicate that the motile density field strongly boosted with the increment in Peclet number and microorganisms Biot number; however, they are suppressed with the increase in the values of bioconvection Schmidt number and motile microorganism concentration difference parameter.
Semantic similarity and analysis of the word frequency dynamics

In this study a similarity in changes of frequencies dynamics for semantically related words was analyzed using word statistics extracted from more than 4.5 million books written over a period of 205 years. The approach is based on the correlation analysis of 1-grams frequency dynamics. We analyzed the frequencies correlation of synonym pairs, their corresponding antonymous groups and random words pairs. Also, we compared several metrics to find the most effective for assessing the degree of similarity in the dynamics of use of different words. Comparing differences between logarithmic rank variations in pairs of synonyms and random word pairs, significant differences are found, though they are smaller than it could be expected.
Deciding Together as Faculty: Narratives of Unanticipated Consequences in Gendered and Racialized Departmental Service, Promotion, and Voting

Abstract Workplace inequalities scholarship often assumes making people aware of problems will lead to change, although gendered and racialized organizations theories show systemic problems beyond individual awareness. Still, not enough research analyzes the narratives of savvy organizational actors – like university faculty aware of inequalities – to understand the mechanisms operating against leveraging that knowledge for change. Data consist of 10 group interviews with 45 faculty across departments in one US public university, supplemented by content analysis of 56 departments’ written bylaws. Findings focus on three common shared decisions: committee service, hiring/promotion, and voting practices. We find awareness of inequality may actually reinforce the status quo when narratives about gendered and racialized processes feature decoupling from formal bylaws, and when narratives about outcomes relate to multiple layers of unanticipated consequences favoring whiteness and men. Specifically, inequality is reproduced when narratives about gendered and racialized unanticipated consequences: 1) highlight the imperviousness of change, as in the difficulty of allocating service work equitably, 2) lack reflexivity and shift responsibility to ‘other’ groups – ‘faculty’ or ‘administrators’ – as in unequal hiring and promotion decisions, and 3) focus on standard old boy stories which obscure other inequalities, as in faculty voting where non-tenure track rank inequality obscures race/gender inequalities. When unanticipated consequences narratives have dimensions of fatalism, finger pointing, and blindness to intersectionality, white men may continue to benefit. This study shows how formal policies and awareness of inequalities may still fail to produce change.
Tunable Direct Bandgap Optical Transitions in MoS2 Nanocrystals for Photonic Devices

Highly luminescent MoS2 nanocrystals (NCs) with controlled size distribution have been achieved using a simple yet inexpensive and impurity free sono-chemical exfoliation method followed by gradient centrifugation. The size of nanocrystals could be varied within the diameter range of ∼4 to 70 nm. Typical MoS2 nanocrystal has exhibited high crystalline quality with 0.25 nm lattice fringe spacing for (002) planes for 2-H phase of MoS2. Raman spectra has revealed that both out-of-plane and in-plane vibrational modes are stiffen due to the edge effect of MoS2 NCs. The size tunable optical properties of MoS2 NCs have been investigated by optical absorption and photoluminescence spectroscopy. The coexistence of direct band gap emission from 2D MoS2 nanosheets and quantum confined nanocrystals has been achieved. A strong and tunable photoluminescence (560–518 nm) emission due to the quantum size effect of tiny NCs below a critical dimension is reported for the first time. The photocurrent measurement of the Au/M.
Deep convolutional neural networks for building extraction from orthoimages and dense image matching point clouds

Abstract. Automatic extraction of buildings from remote sensing data is an attractive research topic, useful for several applications, such as cadastre and urban planning. This is mainly due to the inherent artifacts of the used data and the differences in viewpoint, surrounding environment, and complex shape and size of the buildings. This paper introduces an efficient deep learning framework based on convolutional neural networks (CNNs) toward building extraction from orthoimages. In contrast to conventional deep approaches in which the raw image data are fed as input to the deep neural network, in this paper the height information is exploited as an additional feature being derived from the application of a dense image matching algorithm. As test sites, several complex urban regions of various types of buildings, pixel resolutions and types of data are used, located in Vaihingen in Germany and in Perissa in Greece. Our method is evaluated using the rates of completeness, correctness, and quality and compared with conventional and other “shallow” learning paradigms such as support vector machines. Experimental results indicate that a combination of raw image data with height information, feeding as input to a deep CNN model, provides potentials in building detection in terms of robustness, flexibility, and efficiency.
Marine plankton microscope system based on light field camera

Light Field camera is a kind of device which uses a microlens array to record the four-dimensional light field information in the scene and matches the light with the CCD to realize the function of image refocusing according to given relationship. In this paper, we apply the microlens array in the underwater microscopy system and use microscopic objective, microlens array and CCD to construct an underwater light field microscope. We improve microscopy system which has small depth and is difficult to focus and evaluate effect of microlens array on light field sampling and resolution of refocused images at different positions. In the experiments, we calibrate camera, confirm the magnification and field size and take some photos of marine plankton in the experimental environment.
Mathematical programs with vanishing constraints: constraint qualifications, their applications, and a new regularization method

ABSTRACT We propose a new family of relaxation schemes for mathematical programs with vanishing constraints that extend the relaxation of Hoheisel, Kanzow & Schwartz from 2012. We discuss the properties of the sequence of relaxed non-linear programs as well as stationary properties of limiting points. Our relaxation schemes have the desired property of converging to an M-stationary point. A main advantage of this new method is to converge to an S-stationary point satisfying MPVC-LICQ for a large class of problem. We also study MPVC constraint qualification connected to this study and prove convergence of the method under the new MPVC-CRSC. Additionally, we obtain the new MPVC-wGCQ and prove that it is the weakest MPVC constraint qualification.
Standardization of Thromboelastography: Values and Challenges

Laboratory evaluation of hemostasis has been performed using plasma for several decades. The cell-based model of coagulation has now led to renewed interest in the global assays of coagulation such as thrombin generation and thromboelastography. These tests have remained as research tools, however, because of the lack of studies to demonstrate their reliability. The number of publications in the ﬁeld of thromboelastography is growing daily, and many areas of clinical medicine are targeting the ability of this assay to evaluate in real time the process of coagulation and ﬁbrin polymerization. It is clear that the methods employed by different investigators differ signiﬁcantly, and therefore the results are not comparable. It is therefore critical to standardize the assay to achieve clinical relevance. This article summarizes the TEG-ROTEM Working Group’s efforts to try and stand-ardize thromboelastography and the challenges faced in this process. Although this has been the ﬁrst effort to standardize this test, it is extremely important to continue this work, so that we may investigate the usefulness and possible applications of thromboelastography in evaluating the process of hemostasis.
Brachial Plexus and Nerves about the Shoulder

Ultrasound (US) and MR imaging have been shown able to detect in-depth features of brachial plexus anatomy and to localize pathological lesions in disorders where electrophysiology and physical ﬁndings are nonspeciﬁc or nonlocalizing. High-end gradient technology, phased array coils, and selection of an appropriate protocol of pulse sequences are the main requirements to evaluate the brachial plexus nerves with MR imaging and to distinguish between intrinsic and extrinsic pathological changes. A careful scanning technique based on anatomical landmarks is required to image the brachial plexus nerves with US. In traumatic injuries, MR imaging and myelographic techniques can exclude nerve lesions at the level of neural foramina and at intradural location. Outside the spinal canal, US is an excellent alternative to MR imaging to determine the presence of a lesion, to establish the site and the level of nerve involvement, as well as to conﬁrm or exclude major nerve injuries. In addition to brachial plexus injuries, MR imaging and US can be contributory in a variety of nontraumatic brachial plexopathies of a compressive, neoplastic, and inﬂam-matory nature. In the thoracic outlet syndrome, imaging performed in association with postural maneuvers can help diagnose dynamic compressions. MR imaging and US are also effective to recognize neuropathies about the shoulder girdle involving the suprascapular, axillary, long thoracic, and spinal accessory nerves that may mimic brachial plexopathy. In this article, the clinical entities just listed are discussed independently, providing an overview of the current status of knowledge regarding imaging assessment.
Medical Therapy for Ectopic Pregnancy

Methotrexate for treatment of ectopic tubal pregnancy has become an accepted alternative to surgical options. Methotrexate is a folic acid analog that interferes with DNA synthesis. Protocols using planned multiple doses of methotrexate alternating with citrovorum rescue factor and one protocol using only a single planned dose are both currently used in the treatment of ectopic pregnancy. In remains unclear which protocol is superior. This article reviews the indications, contraindications, and speciﬁcs of using methotrexate for this purpose. Also reviewed are predictors of success and management of usual complications associated with methotrexate therapy.
The Efficacy and Safety of Human Oocyte Vitrification

Vitriﬁcation is now a widely applied and highly successful approach for cryopre-servation in reproductive biology. Rapidly increasing data prove that it is also a highly efﬁcient technique for low-temperature storage of human oocytes. The latest approaches with appropriately selected cryoprotectants, tools and techniques, and properly adjusted parameters allow close to 100% morphological survival rates, and in vitro embryo development, as well pregnancy and implantation rates, comparable with those achieved with fresh oocytes. With standardization of the technique and elimination of biosafety problems by preserving all the positive features, vitriﬁcation may become a common part of the everyday routine in a human embryo laboratory, and it may offer a solution for various medical and social situations as well as for simple logistic problems commonly occurring in assisted reproduction
Functional and Structural Characterization of an IclR Family Transcription Factor for the Development of Dicarboxylic Acid Biosensors

Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work we characterize the PcaR TF belonging to the IclR family. We present in vitro functional analysis of PcaR’s ligand profile and construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this TF. This work provides key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors. Graphical Abstract Highlights PcaR is an IclR family transcription regulator responsive to dicarboxylic acids PcaR was established as an in vivo biosensor in yeast Crystal structure of PcaR in the apo form was solved Crystal structure with PcaR in complex with succinate was solved Sequence alignments unveil ligand-binding positions in the IclR family
Analysis of RyR2 distribution in HEK293 cells and mouse cardiac myocytes using 3D MINFLUX microscopy

The cardiac type 2 ryanodine receptor (RyR2) is a large homotetramer of a ∼560 kD subunit and is the molecular pathway through which the majority of Ca2+ enters the cytosol during cardiac activation. It constitutes the molecular basis of the process of calcium induced calcium release where activation of RyR2s can be locally regenerative giving rise to local release events termed Ca2+ sparks. Accordingly, the molecular distribution of RyR2 in cardiac myocytes has been of great interest. Here we present the first purely optical data of RyR2 distribution with sub-molecular resolution by applying 3D MINFLUX fluorescence super-resolution microscopy. We demonstrate that by using single-domain antibodies (sdABs) against fluorescent protein domains in engineered RyR2 fluorescent protein fusions we can determine the location of individual RyR2 subunits with high precision (∼3 nm) in all directions. This allows determining not only the location but also the 3D orientation of individual RyR2 channels in intact cells. In practice, this capability is currently limited by a relatively modest effective labeling efficiency (∼10 % subunit detection efficiency translating into ∼35% RyR2 labeling efficiency) which we measure in-situ using a novel procedure enabled by the true molecular resolution of MINFLUX microscopy. The new data suggests a resolution to apparent discrepancies between previous data from electron microscopy and super-resolution data that may be at least partially explained by effects of labeling efficiency. The methodology developed here will be critical to reveal the full complexity of RyR2 and related Ca2+ handling proteins in 3D as well as their relationship to contractile function. Our new approaches may be applicable to other multi-subunit complexes in cardiac muscle and other cell types.