Miracle-dz/UniFAR-FTUs huggingface dataset:
A comparative study on prominent nature inspired algorithms for function optimization

Optimization includes finding best available values of some objective function given a defined domain. Function optimization (FO) is the well-studied continuous optimization task which aim is to find best suited parameter values to get optimal value of a function. A number of techniques have been investigated in last few decades to solve FO and recently Nature Inspired Algorithms (NIAs) become popular to solve it. The objective of this study is to draw a fair comparison among prominent NIAs in solving benchmark test functions. Algorithms we selected are Genetic Algorithm (GA), Particle Swarm Optimization (PSO), Artificial Bee Colony (ABC) optimization, Firefly Algorithm (FFA), Cuckoo Search Optimization (CSO), Group Search Optimization (GSO) and Grey Wolf Optimizer (GWO). Among the methods, GA is the pioneer method for optimization, PSO is the most popular in recent time and GWO is the most recently developed method. Experimental results revealed that GWO is the overall best method among the NIAs and PSO is still promising to solve bench mark functions.
Disruption of CXCR2-Mediated MDSC Tumor Trafficking Enhances Anti-PD1 Efficacy

Preventing trafficking of myeloid-derived suppressor cells to the tumor site enhances the efficiency of checkpoint blockade. Cross-Checking Cancer Immunological checkpoint blockades are a promising approach in cancer immunotherapy—pushing the immune response to the tumor past tolerance into attack mode. Now, Highfill et al. show that inhibiting myeloid-derived suppressor cells by preventing their trafficking into the tumor site can enhance the efficiency of checkpoint blockade. They found in a mouse model of rhabdomyosarcoma that blocking a chemokine receptor on myeloid-derived suppressor cells in conjunction with antibodies to the checkpoint molecule programmed death 1 induced substantial antitumor effects. Moreover, patients with rhabdomyosarcoma that had elevated levels of ligands for this chemokine receptor had poorer prognosis. These data suggest that combining these therapies may increase the likelihood of patient response, checking cancer into the boards. Suppression of the host’s immune system plays a major role in cancer progression. Tumor signaling of programmed death 1 (PD1) on T cells and expansion of myeloid-derived suppressor cells (MDSCs) are major mechanisms of tumor immune escape. We sought to target these pathways in rhabdomyosarcoma (RMS), the most common soft tissue sarcoma of childhood. Murine RMS showed high surface expression of PD-L1, and anti-PD1 prevented tumor growth if initiated early after tumor inoculation; however, delayed anti-PD1 had limited benefit. RMS induced robust expansion of CXCR2+CD11b+Ly6Ghi MDSCs, and CXCR2 deficiency prevented CD11b+Ly6Ghi MDSC trafficking to the tumor. When tumor trafficking of MDSCs was inhibited by CXCR2 deficiency, or after anti-CXCR2 monoclonal antibody therapy, delayed anti-PD1 treatment induced significant antitumor effects. Thus, CXCR2+CD11b+Ly6Ghi MDSCs mediate local immunosuppression, which limits the efficacy of checkpoint blockade in murine RMS. Human pediatric sarcomas also produce CXCR2 ligands, including CXCL8. Patients with metastatic pediatric sarcomas display elevated serum CXCR2 ligands, and elevated CXCL8 is associated with diminished survival in this population. We conclude that accumulation of MDSCs in the tumor bed limits the efficacy of checkpoint blockade in cancer. We also identify CXCR2 as a novel target for modulating tumor immune escape and present evidence that CXCR2+CD11b+Ly6Ghi MDSCs are an important suppressive myeloid subset in pediatric sarcomas. These findings present a translatable strategy to improve the efficacy of checkpoint blockade by preventing trafficking of MDSCs to the tumor site.
Evaluating performance of reconstruction algorithms for 3D O-15 water PET using subtraction analysis

Positron emission tomography (PET) [15O] activation studies have benefited significantly from three-dimensional (3-D) data acquisition. However, they have been slow to take advantage of new 3-D reconstruction techniques. Compared with the widely used 3-D reprojection reconstruction (3DRP), the advantage of signal and noise for iterative algorithms has been outweighed by concern about long and complicated reconstruction procedures and inconsistent performance. Most pseudo-3-D algorithms, such as rebinning methods, aim at increasing the speed of reconstruction but lack further resolution improvement or noise control. Although many evaluations have been conducted through simulations and phantom experiments, the spatially varying nature of signal and noise and the complexity of biological effects have complicated the interpretation of real data based on simulation or phantom results. We have taken a different approach and used the analysis of real data directly as a measure with which to compare three reconstruction algorithms: 3DRP, iterative filtered backprojection with median root prior (IFBP-MRP), and Fourier rebinning followed by two-dimensional (2-D) filtered backprojection (FORE-FBP) for [15O] PET. Two subjects, each with 32 scans acquired in four sessions during a finger opposition motor task, are analyzed using subtraction. A fixed volume-of-interest (VOI) measurement in regions related to the task demonstrates that at high resolution, IFBP-MRP has the best signal-to-noise performance followed by 3DRP and FORE-FBP; however, this advantage gradually diminishes as the resolution decreases. For a voxel measurement derived from the image of each reconstruction, all three algorithms are capable of detecting highly activated regions. Although there are some differences in the size, shape, and center location of the activated foci, our preliminary results suggest that IFBP-MRP does offer enhanced signal with some noise control compared with 3DRP for the analysis of high-resolution images. If images are to be analyzed at an intermediate to lower resolution, FORE-FBP provides a significant reduction of reconstruction time compared with 3DRP.
Design of photonic sensors based on cavities and new interrogation techniques

Optical sensors are photonic devices sensitive to different magnitudes that are used precisely to measure, in an absolute or a relative way, these magnitudes. These optical sensors are nowadays used to measure temperature, pressure, strain, humidity or the presence of a particular gas. In the past few decades a multitude of photonic sensors and different interrogation techniques have been developed, which had a great impact in dozens of different fields. One of the best examples is civil architecture, in which photonic sensors play a fundamental role in order to monitor the condition of the structures. Despite of the good results showed by photonic sensors, the interrogation techniques used show different drawbacks. A large measurement time, low resolution or great complexity are some of them. In this doctoral thesis the design and characterization of a set of different photonic sensors based on the already known fiber Bragg gratings, along with the implementation of new interrogation techniques, are used in order to eliminate or at least reduce these problems. The interrogation techniques developed in this work are based on Microwave Photonics techniques, in which the interaction between optical and electrical signals is used to detect in this case the changes in a particular magnitude. The techniques showed in this work have been designed in order to be as versatile and scalable as possible to have the opportunity to adapt to any requirement in different scenarios. In this work techniques that are able to interrogate hundreds or even thousands of sensors with great sensitivity and resolution can be found in addition to techniques that are developed to interrogate individual sensors with an enormous sensitivity. The work carried out in collaboration with the Swedish research institute ACREO, based on the development of an electric field sensor based on poled fibers together with FBGs is also present.
Injuries Among Spanish Male Amateur Soccer Players

Background: Soccer is the most popular sport worldwide, with about 265 million players, both professionals and amateurs. Most research investigating soccer injuries has focused on professional players because they have greater exposure time, but most soccer players are at the recreational level. Purpose: To undertake a retrospective epidemiological study of the injuries sustained in Spanish amateur soccer during the 2010-2011 season. Study Design: Descriptive epidemiological study. Methods: Any injuries incurred by the 134,570 recreational soccer players (aged 18-55 years) registered with the Spanish Football Federation were reported to the federation’s medical staff. A standardized medical questionnaire, based on the Fédération International de Football Association (FIFA) Medical and Research Centre (F-MARC) consensus for collection procedures in studies of soccer injuries, was used to classify the injury according to type, severity, location, and treatment. Results: A total of 15,243 injuries were reported, with an average of 0.11 injuries per player and per year. From the total number of injuries, 67.2% were classified as injuries that resulted in time loss, while the remaining 32.7% were injuries that required medical attention. Most injuries led to a minimum of 1 competitive match being missed (87%), and only 2.5% were recurrent injuries. The rate of injuries per 1000 hours of play was double during games (1.15/1000 hours) compared with during training (0.49/1000 hours). From the total number of injuries reported, 7.7% corresponded to goalkeepers, 24.2% to forwards, 33.8% to defenders, and 34.3% to midfielders. The knee (29.9%) and ankle joints (12.4%) were the most common body locations injured, while ligament sprains and ruptures accounted for 32.1% of the total injuries attended. Older amateur players (age ≥30 years) had a greater number of injuries per year and per 1000 hours of play than their younger counterparts. Conclusion: The risk of injury in amateur soccer is lower than that previously reported in professional players. The most common complaints in amateur players are knee ligament injuries. Further research is needed to investigate ways of reducing the incidence of injuries in amateur soccer.
Diffuse large cell lymphomas are derived from mature B cells carrying V region genes with a high load of somatic mutation and evidence of selection for antibody expression

In the Revised European American Lymphoma (REAL) classification, several subtypes of high‐grade lymphomas were combined in the entity diffuse large cell lymphoma (DLL). In the present study, a total of 19 cases of DLL (10 cases of centroblastic lymphoma, 5 cases of mediastinal B cell lymphoma, 2 cases of immunoblastic lymphoma, 1 case of T cell‐rich B lymphoma and one case of large cell anaplastic lymphoma) were analyzed for somatically mutated immunoglobulin V region genes. Somatic mutations are acquired in the course of the germinal center (GC) reaction and are thus found in GC B cells and their descendants, i.e. memory B cells. The V gene sequences revealed that the tumor cells of all five subtypes of DLL harbored mutated V region genes and are thus derived from antigen‐experienced (post) GC B cells. This indicates that from the point of view of the stage of development of the tumor precursor, the combination of those five subtypes to one entity, i.e. DLL, seems reasonable. In some cases, an unusually high frequency of somatic mutations was detected. This may indicate that DLL are derived from GC B cells, which, due to transforming events, stayed in the GC for prolonged periods of time, thereby accumulating a high load of somatic mutation. An analysis of the mutation pattern suggests that the tumor clone or its precursor were selected for antibody expression while acquiring somatic mutations. The latter observation discriminates DLL from classical Hodgkin's disease, where we recently also observed a high load of somatic mutation within rearranged V region genes, but a frequent occurrence of crippling mutations.
Expression recognition in the wild with transfer learning

Expression recognition in the wild is a challenging task because of the interference of various environment. In this paper, we propose a transfer-learning method that utilize two representative transformations from grayscale images as input and fuse their results in decision level to enhance the overall performance, which also address the dimensional mismatch issue when applying pre-trained deep neural network on grayscale images. Each network consists of the body of pre-trained deep network which is freezed during training process, and two other layers that trained for our expression classification task. Our method achieve an accuracy of 63.72%, a 11.18% improvement over baseline results on FER-2013 with fewer computation compared with other deep-learning methods, which demonstrate the complementary effect between two different inputs, as well as the good generalization ability of the features extracted by pre-trained network.
Preoperative Prediction of Ambulatory Status at 6 Months After Total Hip Arthroplasty

Background Total hip arthroplasty (THA) is an effective procedure that provides patients with long-term relief from pain and enables them to resume their normal daily activities. Preoperative instruction about the functional outcomes and optimum goal of rehabilitation is helpful for patients undergoing THA. Objective The purposes of this study were: (1) to examine the relationships between preoperative physical functions and ambulation following THA and (2) to identify optimal cutoff values for estimating ambulatory status at 6 months after THA. Design This was a retrospective study. Methods The study participants were 204 patients who underwent a unilateral THA. Hip abductor and knee extensor strength were measured and the Timed “Up & Go” Test (TUG) was conducted preoperatively. The patients were divided into 2 groups according to self-reported walking ability at 6 months postoperatively: an independent ambulation group (n=118) and a cane-assisted ambulation group (n=86). Differences between the 2 groups were examined using an unpaired t test or the chi-square test. A stepwise multiple logistic regression analysis was performed with walking ability at 6 months postoperatively as a dependent variable and age, sex, contralateral hip osteoarthritis (ie, whether a participant had contralateral hip osteoarthritis or not), body mass index, hip abductor strength, knee extensor strength, and TUG score as independent variables. Receiver operating characteristic curve analysis was used to identify a cutoff point for classifying the participants into the 2 groups. Results A stepwise multiple logistic regression analysis selected 3 factors (age, knee extensor strength, and TUG score) as significant variables affecting the midterm ambulatory ability after THA. Moreover, receiver operating characteristic curve analyses revealed that the midterm (ie, 6-month) ambulatory status after THA was more accurately predicted by the patient's TUG score (cutoff point=10 seconds, sensitivity=76.7%, specificity=93.2%, area under the curve=0.93) than by age and knee extensor strength. Limitations The categorization of ambulatory status in this study was based solely on self-reported walking ability. Conclusion The findings indicate that patients with a preoperative TUG score of less than 10 seconds are likely to walk without an assistive device at 6 months after THA.
Functional coexistence of twin arsenic resistance systems in Pseudomonas putida KT2440.

The genome of the soil bacterium Pseudomonas putida KT2440 bears two virtually identical arsRBCH operons putatively encoding resistance to inorganic arsenic species. Single and double chromosomal deletions in each of these ars clusters of this bacterium were tested for arsenic sensitivity and found that the contribution of each operon to the resistance to the metalloid was not additive, as either cluster sufficed to endow cells with high-level resistance. However, otherwise identical traits linked to each of the ars sites diverged when temperature was decreased. Growth of the various mutants at 15°C (instead of the standard 30°C for P. putida) uncovered that ars2 affords a much higher resistance to As (III) than the ars1 counterpart. Reverse transcription polymerase chain reaction of arsB1 and arsB2 genes as well as lacZ fusions to the Pars1 and Pars2 promoters traced the difference to variations in transcription of the corresponding gene sets at each temperature. Functional redundancy may thus be selected as a stable condition - rather than just as transient state - if it affords one key activity to be expressed under a wider range of physicochemical settings. This seems to provide a straightforward solution to regulatory problems in environmental bacteria that thrive under changing scenarios.
Contribution of Trabecular and Cortical Components to Biomechanical Behavior of Human Vertebrae: An Ex Vivo Study

Whereas there is clear evidence for a strong influence of bone quantity (i.e., bone mass or bone mineral density) on vertebral mechanical behavior, there are fewer data addressing the relative influence of cortical and trabecular bone microarchitecture. The aim of this study was to determine the relative contributions of bone mass, trabecular microarchitecture, and cortical thickness and curvature to the mechanical behavior of human lumbar vertebrae. Thirty‐one L3 vertebrae (16 men, 15 women, aged 75 ± 10 years and 76 ± 10 years, respectively) were obtained. Bone mineral density (BMD) of the vertebral body was assessed by lateral dual energy X‐ray absorptiometry (DXA), and 3D trabecular microarchitecture and anterior cortical thickness and curvature was assessed by micro‐computed tomography (µCT). Then compressive stiffness, work to failure, and failure load were measured on the whole vertebral body. BMD was correlated with compressive stiffness (r = 0.60), failure load (r = 0.70), and work to failure (r = 0.55). Except for the degree of anisotropy, all trabecular and cortical parameters were correlated with mechanical behavior (r = 0.36 to 0.58, p = .05 to .001, and r = 0.36 to 0.61, p = .05 to .0001, respectively). Stepwise and multiple regression analyses indicated that the best predictor of (1) failure load was the combination of BMD, structural model index (SMI), and trabecular thickness (Tb.Th) (R = 0.80), (2) stiffness was the combination of BMD, Tb.Th, and curvature of the anterior cortex (R = 0.82), and (3) work to failure was the combination of anterior cortical thickness and BMD (R = 0.68). Our data imply that measurements of cortical thickness and curvature may enhance prediction of vertebral fragility and that therapies that improve both vertebral cortical and trabecular bone properties may provide a greater reduction in fracture risk. © 2010 American Society for Bone and Mineral Research
Epilepsy-associated KCNQ2 channels regulate multiple intrinsic properties of Layer 2/3 pyramidal neurons.

KCNQ2 potassium channels are critical for normal brain function, as both loss- and gain-of-function KCNQ2 variants can lead to various forms of neonatal epilepsy. Despite recent progress, the full spectrum of consequences as a result of KCNQ2 dysfunction in neocortical pyramidal neurons is still unknown. Here, we report that conditional ablation of Kcnq2 from mouse neocortex leads to hyperexcitability of layer 2/3 (L2/3) pyramidal neurons, exhibiting an increased input resistance and action potential frequency, as well as a reduced medium afterhyperpolarization (mAHP), a conductance partly mediated by KCNQ2 channels. Importantly, we show that introducing the KCNQ2 loss-of-function variant KCNQ2(I205V) into L2/3 pyramidal neurons using in utero electroporation also results in a hyperexcitable phenotype similar to the conditional knockout. KCNQ2(I205V) has a right-shifted conductance-to-voltage relationship, suggesting loss of KCNQ2 channel activity at subthreshold membrane potentials is sufficient to drive large changes in L2/3 pyramidal neuronal excitability even in the presence of an intact mAHP. We also found that the changes in excitability following Kcnq2 ablation are accompanied by alterations at action potential properties including action potential amplitude in Kcnq2-null neurons. Importantly, partial inhibition of Nav1.6 channels was sufficient to counteract the hyperexcitability of Kcnq2-null neurons. Therefore, our work shows that loss of KCNQ2 channels alters the intrinsic neuronal excitability and action potential properties of L2/3 pyramidal neurons, and identifies Nav1.6 as a new potential molecular target to reduce excitability in patients with KCNQ2 encephalopathy. SIGNIFICANCE STATEMENT KCNQ2 channels are critical for the development of normal brain function, as KCNQ2 variants could lead to epileptic encephalopathy. However, the role of KCNQ2 channels in regulating the properties of neocortical neurons is largely unexplored. Here, we find that Kcnq2 ablation or loss-of-function at subthreshold membrane potentials leads to increased neuronal excitability of neocortical L2/3 pyramidal neurons. We also demonstrate that Kcnq2 ablation unexpectedly leads to a larger action potential amplitude. Importantly, we propose the Nav1.6 channel as a new molecular target for patients with KCNQ2 encephalopathy, as partial inhibition of these channels counteracts the increased L2/3 pyramidal neuron hyperexcitability of Kcnq2-null neurons.
Natural Outbreak of BVDV-1d–Induced Mucosal Disease Lacking Intestinal Lesions

Bovine viral diarrhea virus (BVDV) belongs to the Pestivirus genus, which is further divided into subgenotypes (1a–1u and 2a–c). When persistent infection occurs, the calf will be immunotolerant to BVDV and possibly develop mucosal disease. This study describes an outbreak of BVDV-1d–induced mucosal disease lacking intestinal lesions. Eleven calves presented with anorexia, sialorrhea, lameness, recumbency, and death. Three calves were necropsied, showing ulceration of the interdigital skin and the oral and nasal mucosa; linear ulcers in the tongue, esophagus, and rumen; and rounded ulcers in the abomasum. Microscopically, mucosa and skin had superficial necrosis, with single-cell necrosis and vacuolation in epithelial cells, and severe parakeratosis. Immunohistochemistry (IHC) showed BVDV antigen in the cytoplasm of epithelial cells in skin and mucosa. All 11 dead calves were positive upon reverse transcription-polymerase chain reaction (RT-PCR) for the detection of Pestivirus along with another 11 live calves from the herd, which were positive again by RT-PCR and IHC after a 4-week interval. Sequencing of the 5′ untranslated region and N-terminal protease showed that viruses from these 22 calves were homologous and of subgenotype BVDV-1d. Cytopathic BVDV was isolated from 8 of 11 dead calves, but only noncytopathic BVDV was isolated from the 11 live animals. The findings indicate that this was an outbreak of mucosal disease caused by BVDV-1d, with high morbidity, and lesions restricted to the upper alimentary system and skin and absent from intestine. Thus, the epidemiological and pathological features in this form of mucosal disease may be similar to vesicular diseases, including foot and mouth disease.