Miracle-dz/UniFAR-FTUs huggingface dataset:
Lentivirus Display: Stable Expression of Human Antibodies on the Surface of Human Cells and Virus Particles

Background Isolation of human antibodies using current display technologies can be limited by constraints on protein expression, folding and post-translational modifications. Here we describe a discovery platform that utilizes self-inactivating (SIN) lentiviral vectors for the surface display of high-affinity single-chain variable region (scFv) antibody fragments on human cells and lentivirus particles. Methodology/Principal Findings Bivalent scFvFc human antibodies were fused in frame with different transmembrane (TM) anchoring moieties to allow efficient high-level expression on human cells and the optimal TM was identified. The addition of an eight amino acid HIV-1 gp41 envelope incorporation motif further increased scFvFc expression on human cells and incorporation into lentiviral particles. Both antibody-displaying human cells and virus particles bound antigen specifically. Sulfation of CDR tyrosine residues, a property recently shown to broaden antibody binding affinity and antigen recognition was also demonstrated. High level scFvFc expression and stable integration was achieved in human cells following transduction with IRES containing bicistronic SIN lentivectors encoding ZsGreen when scFvFc fusion proteins were expressed from the first cassette. Up to 106-fold enrichment of antibody expressing cells was achieved with one round of antigen coupled magnetic bead pre-selection followed by FACS sorting. Finally, the scFvFc displaying human cells could be used directly in functional biological screens with remarkable sensitivity. Conclusions/Significance This antibody display platform will complement existing technologies by virtue of providing properties unique to lentiviruses and antibody expression in human cells, which, in turn, may aid the discovery of novel therapeutic human mAbs.
Quantitative proteome profiling of lymph node‐positive vs. ‐negative colorectal carcinomas pinpoints MX1 as a marker for lymph node metastasis

We used high‐resolution mass spectrometry to measure the abundance of more than 9,000 proteins in 19 individually dissected colorectal tumors representing lymph node metastatic (n = 10) and nonmetastatic (n = 9) phenotypes. Statistical analysis identified MX1 and several other proteins as overexpressed in lymph node‐positive tumors. MX1, IGF1‐R and IRF2BP1 showed significantly different expression in immunohistochemical validation (Wilcoxon test p = 0.007 for IGF1‐R, p = 0.04 for IRF2BP1 and p = 0.02 for MX1 at the invasion front) in the validation cohort. Knockout of MX1 by siRNA in cell cultures and wound healing assays provided additional evidence for the involvement of this protein in tumor invasion. The collection of identified and quantified proteins to our knowledge is the largest tumor proteome dataset available at the present. The identified proteins can give insights into the mechanisms of lymphatic metastasis in colorectal carcinoma and may act as prognostic markers and therapeutic targets after further prospective validation.
A Multipopulation PSO Based Memetic Algorithm for Permutation Flow Shop Scheduling

The permutation flow shop scheduling problem (PFSSP) is part of production scheduling, which belongs to the hardest combinatorial optimization problem. In this paper, a multipopulation particle swarm optimization (PSO) based memetic algorithm (MPSOMA) is proposed in this paper. In the proposed algorithm, the whole particle swarm population is divided into three subpopulations in which each particle evolves itself by the standard PSO and then updates each subpopulation by using different local search schemes such as variable neighborhood search (VNS) and individual improvement scheme (IIS). Then, the best particle of each subpopulation is selected to construct a probabilistic model by using estimation of distribution algorithm (EDA) and three particles are sampled from the probabilistic model to update the worst individual in each subpopulation. The best particle in the entire particle swarm is used to update the global optimal solution. The proposed MPSOMA is compared with two recently proposed algorithms, namely, PSO based memetic algorithm (PSOMA) and hybrid particle swarm optimization with estimation of distribution algorithm (PSOEDA), on 29 well-known PFFSPs taken from OR-library, and the experimental results show that it is an effective approach for the PFFSP.
Simulating Multiple Character Interactions with Collaborative and Adversarial Goals

This paper proposes a new methodology for synthesizing animations of multiple characters, allowing them to intelligently compete with one another in dense environments, while still satisfying requirements set by an animator. To achieve these two conflicting objectives simultaneously, our method separately evaluates the competition and collaboration of the interactions, integrating the scores to select an action that maximizes both criteria. We extend the idea of min-max search, normally used for strategic games such as chess. Using our method, animators can efficiently produce scenes of dense character interactions such as those in collective sports or martial arts. The method is especially effective for producing animations along story lines, where the characters must follow multiple objectives, while still accommodating geometric and kinematic constraints from the environment.
Identification of Unique Lipoprotein Subclasses for Visceral Obesity by Component Analysis of Cholesterol Profile in High-Performance Liquid Chromatography

Objective—The contribution of visceral fat accumulation to the development of coronary heart disease was previously reported, but the relation between visceral fat accumulation and serum lipoprotein subclasses was unknown. Methods and Results—We examined the relation of lipoprotein subclasses with visceral fat accumulation in 62 male subjects (aged 22 to 67 years) with visceral fat syndrome or obesity. Cholesterol levels in very low–density, low-density, and high-density lipoprotein subclasses (VLDL, LDL, and HDL) were determined by computer-assisted high-performance liquid chromatography. Subcutaneous fat area and visceral fat area were measured by computed tomographic scanning. There was no significant correlation between the subcutaneous fat area and the cholesterol levels in all lipoprotein subclasses. In contrast, the visceral fat area was correlated positively (P<0.002) with VLDL and LDL subclasses, except for large LDL, but negatively (P<0.001) with those in large and medium HDL subclasses. The observed positive correlations of small and very small LDL subclasses remained significant (P<0.005) after adjustment for serum cholesterol, triglycerides, HDL cholesterol, and LDL cholesterol, respectively, but a significant negative correlation (P<0.005) of large LDL was obtained after adjustment for LDL cholesterol. Conclusion—These findings indicate that this simple high-performance liquid chromatography method may be applied for easy detection and evaluation of abnormal distribution of lipoprotein subclasses.
Deformation transfer based on stretchiness ratio

In this paper we propose a deformation transfer technique that achieves physically-plausible deformation by transferring stretchiness ratios of local edges. Given a source reference mesh, a source deformed mesh, and a target reference mesh, the objective is to transfer deformation between the source reference and deformed onto the target reference, and produce a target deformed mesh. To generate a deformed target, we create a mass-spring system which is topologically consistent with the target reference mesh and multiply the stretchiness ratio between the edge lengths from the source meshes to the rest lengths of that mass-spring system. The deformed new target mesh can be synthesized by computing the equilibrium state of the new mass-spring system. To increase the performance we also adopt a non-linear multi-grid algorithm for solving large scale mass-spring systems. Stretchiness ratio is a coordinate-free quantity and we show that our method outperform previous approaches in certain cases.
Large Scale Parallel Hybrid GMRES Method for the Linear System on Grid System

The method GMRES is used widely to solve the large sparse linear systems. In this paper, we will present an effective parallel hybrid asynchronous method, which combines the typical parallel method GMRES with the Least Square method that needs some eigenvalues obtained from a parallel Arnoldi process. And we will apply it on a Grid Computing platform Grid5000. Grid computing in general is a special type of parallel computing. It intends to deliver high-performance computing over distributed platforms for computation and data-intensive applications by making use of a very large amount of resources. From the numeric results, we will present this hybrid method has some advantage for some matrices compared to the general method GMRES.
Iron acquisition during growth in an iron-deficient medium by Rhizobium sp. isolated from Cicer arietinum

A catechol-type siderophore was produced extracellularly by Rhizobium sp. strain BICC 651 isolated from Cicer arietinum during growth in iron-deficient medium. Production of the siderophore was fully repressed in the presence of 50 μM Fe3+. The siderophore was purified and characterized as containing 2,3-dihydroxybenzoic acid (DHBA) as the core compound and threonine as its conjugate. The siderophore was able to reverse growth inhibition of the strain induced by ethylenediamine-di(o-hydroxyphenyl-acetic acid) (EDDA). A high-affinity iron-transport system capable of transporting 59Fe-siderophore complex was also induced in Rhizobium BICC 651 grown under iron deficiency. Two protein bands of molecular masses 76 and 82 kDa were also inductively synthesized in the outer membrane of the cells. A partially purified ferrireductase enzyme of Rhizobium BICC 651 catalysed reductive release of iron from the ferric chelate of DHBA. The enzyme had a K m of 0.3 mM for ferri-DHBA, was constitutive in nature, and was present in the cytosolic fraction during growth under both iron-deficient and iron-sufficient conditions. The enzyme occurred as two isoenzymes with R F values of 0.48 and 0.51, respectively, in a nondenaturing polyacrylamide gel.
Percutaneous closure of an incompetent aortic valve using an occluder device in a patient with left ventricular assist device.

November 2013 • Volume 117 • Number 5 CASE PRESENTATION A 56-year-old man with a history of ischemic cardiomyopathy status post–HeartMate II® axial-flow left ventricular assist device (LVAD) placement was admitted to our institution with symptoms of cardiogenic shock. His workup revealed newonset severe aortic insufficiency (AI) (Video 1, see Supplemental Digital Content 1, http://links.lww.com/AA/A589). Because of severe coagulopathy from hepatic failure, the patient was considered a poor candidate for surgical aortic valve (AV) closure. Instead, a novel procedure was devised using a percutaneous septal occluder device to anatomically close the AV. The patient consented to publication of this report. The patient underwent general anesthesia and endotracheal intubation. Intraoperatively before the procedure, a focused transesophageal echocardiography (TEE) examination revealed the following: (1) A continuous eccentric jet of severe AI; (2) An aortic annulus diameter of 24 mm; (3) A sinus of Valsalva diameter of 31 mm; (4) Patent left and right coronary ostia; (5) Moderately reduced right ventricular function; and (6) Severely dilated left ventricle with severely reduced function. After gaining femoral arterial access, a guidewire was advanced under fluoroscopy. Then using TEE, the delivery catheter containing a 25-mm diameter Amplatzer® cribriform septal occluder (St. Jude Medical Corp., St. Paul, MN) was visualized passing through the AV. Before deployment, LVAD flow was temporarily decreased to 1 L/min to reduce the trans-AV gradient and prevent shifting or embolization of the device. Next, the distal disk of the device was deployed within the left ventricular outflow tract (LVOT) (Fig. 1). Last, the proximal disk was deployed within the sinus of Valsalva and delivery catheter removed. After the procedure, repeat TEE examination revealed: (1) Proper device position, with the narrow waist of the double disk resting within the AV (Fig. 2/Video 2, see Supplemental Digital Content 2, http://links.lww.com/AA/A590); (2) No residual AI identified via color flow Doppler (Fig. 3/Video 3, see Supplemental Digital Content 3, http://links.lww. com/AA/A591); (3) Normal mitral function; 4) Patent left coronary ostium but poorly visualized right coronary ostium because of acoustic shadowing from the device; (5) Unchanged right ventricular function; and (6) Reduced left ventricular dilation with unchanged function. After successful completion of the procedure, the patient was tracheally extubated and transported to the intensive care unit. He had complete resolution of his symptoms and was discharged home 5 days later. The patient continues to do well 6 months postprocedure.
Prospective assessment of body weight and body composition changes in patients with psoriasis receiving anti‐TNF‐α treatment

Tumor necrosis factor (TNF)‐α is a pro‐inflammatory cytokine associated with psoriasis pathogenesis. Anti‐TNF‐α therapies are effective in psoriasis. A significant weight gain has been reported in patients treated with anti‐TNF‐α agents. The aim of the present study was to evaluate the body composition changes in psoriatic patients receiving anti‐TNF‐α therapies according with disease phenotype. Forty patients affected with psoriasis were followed up for 24 weeks and divided into two groups: psoriasis vulgaris (PsO) and psoriatic arthritis (PsA). Anthropometric, blood biochemical, body composition parameters, resting metabolic rate, and disease activity indexes were measured at baseline and at week 24. After 24 weeks of anti‐TNF‐α administration, the disease activity indexes and concentration of inflammatory markers were significantly decreased. Seventy‐five percent of PsO and 60% of PsA patients had an increase in body weight. Weight changes correlated with fat mass gain in the PsO group, and with fat and lean mass gain in the PsA group. In the present study, we demonstrated that a blockage of TNF‐α bioactivity is related with fat and lean mass gain in both PsO and PsA subjects. The anti‐TNF‐α therapies could play a key role in the cross talk between adipose tissue and skeletal muscle, mediated by the reduction of TNF‐α and interleukin‐6 production.
BSE-associated Prion-Amyloid Cardiomyopathy in Primates

Prion amyloidosis occurred in the heart of 1 of 3 macaques intraperitoneally inoculated with bovine spongiform encephalopathy prions. This macaque had a remarkably long duration of disease and signs of cardiac distress. Variant Creutzfeldt-Jakob disease, caused by transmission of bovine spongiform encephalopathy to humans, may manifest with cardiac symptoms from prion-amyloid cardiomyopathy.
Using virtualization for online kernel profiling, code coverage and instrumentation

Kernel development is considered more challenging than user space development, partly due the lack of adequate development tools. We present LgDb, an innovative framework for kernel profiling, code coverage and instrumentation. LgDb is built on top of Lguest and allows running inspected kernel modules on virtual environment. The innovation lies on the fact that Lguest hypervisor takes active part in the kernel development process. Unlike previous approaches, that used standard kernel profilers on a guest, we enlist the hypervisor to our aid to achieve better profiling of inspected kernel modules. LgDb strives to provide generic environment for running performance evaluation and checking decision coverage for any inspected kernel module.
Sub-100 nm Si nanowire and nano-sheet array formation by MacEtch using a non-lithographic InAs nanowire mask

We report a non-lithographical method for the fabrication of ultra-thin silicon (Si) nanowire (NW) and nano-sheet arrays through metal-assisted-chemical-etching (MacEtch) with gold (Au). The mask used for metal patterning is a vertical InAs NW array grown on a Si substrate via catalyst-free, strain-induced, one-dimensional heteroepitaxy. Depending on the Au evaporation angle, the shape and size of the InAs NWs are transferred to Si by Au-MacEtch as is (NWs) or in its projection (nano-sheets). The Si NWs formed have diameters in the range of ∼25–95 nm, and aspect ratios as high as 250 in only 5 min etch time. The formation process is entirely free of organic chemicals, ensuring pristine Au–Si interfaces, which is one of the most critical requirements for high yield and reproducible MacEtch.
Resistance of Enterococcus faecium to neutrophil-mediated phagocytosis

During a previous study of the opsonic requirements for neutrophil (polymorphonuclear leukocyte [PMN])-mediated killing of enterococci, we identified two strains of Enterococcus faecium (TX0015 and TX0016) that were resistant to PMN-mediated killing. To better define the mechanism of this resistance, we examined phagocytosis with a fluorescence assay and found that TX0016 was completely resistant to phagocytosis by PMNs; this finding was confirmed by electron microscopy. Examination of multiple strains of enterococci revealed that all 20 strains of Enterococcus faecalis tested were readily phagocytosed (mean, 18 intracellular organisms per PMN; range, 7 to 28). In contrast, only 13 (50%) of 26 strains of E. faecium tested were susceptible to phagocytosis (> or = 7 organisms per PMN); the other 13 strains showed < or = 3 organisms per PMN. Enterococcus casseliflavus ATCC 25788 and one strain of Enterococcus hirae were also resistant to phagocytosis, while two strains of Enterococcus durans, Enterococcus mundtii ATCC 43186, and one strain each of Enterococcus raffinosus and Enterococcus solitarius were readily phagocytosed. Exposure of E. faecium TX0016 to sodium periodate, but not to the protease trypsin or pronase or to phospholipase C, eliminated resistance to phagocytosis. Sialic acid, a common periodate-sensitive structure used by microorganisms to resist opsonization, could not be demonstrated in E. faecium TX0016 by the thiobarbituric acid method, nor was phagocytosis of TX0016 altered by neuraminidase treatment. This study suggests that there is a difference in susceptibility to phagocytosis by PMNs between different species of enterococci and that a carbohydrate-containing moiety which is not sialic acid may be involved in the resistance of E. faecium TX0016 to phagocytosis.
Targeted hepatocellular carcinoma therapy: transferrin modified, self-assembled polymeric nanomedicine for co-delivery of cisplatin and doxorubicin

Abstract Background: Targeted hepatocellular carcinoma (HCC) therapy was carried out to improve the efficacy of liver cancers. The aim of this study was to develop transferrin (Tf) modified, self-assembled polymeric nanoparticles for co-delivery doxorubicin (DOX) and cisplatin (DDP), to achieve combination tumor therapy. Methods: Tf modified polyethylene glycol (PEG) containing DOX prodrug (Tf-PEG-DOX) was synthesized. DDP containing poly(lactic-co-glycolic) acid (PLGA) materials (PLGA-DDP) were prepared. Tf modified DOX and DDP loaded PLGA nanoparticles (Tf-DOX/DDP NPs) were prepared by using nanoprecipitation method. The particles sizes, zeta potentials, drug loading effects were characterized. The cytotoxicity of the NPs was evaluated in human hepatoma carcinoma cell lines (HepG2 cells), and in vivo anti-tumor was observed in mice bearing human HepG2 cells model. Results: Tf-DOX/DDP NPs displayed higher cytotoxicity and enhanced antitumor activity both in vitro and in vivo over their non-modified and single drug loaded counterparts. Conclusion: Tf-DOX/DDP NPs can achieve outstanding anti-tumor activity due to the combination effect of two drugs and the active targeting ability of Tf ligands. The self-assembled polymeric nanomedicine could act as an efficient therapy method for HCC treatment.
Myofascial Pain Syndrome in the Elderly and Self-Exercise: A Single-Blind, Randomized, Controlled Trial.

OBJECTIVE This study aimed to demonstrate the effect of self-exercise with a therapeutic inflatable ball (SEIB) in elderly patients with myofascial pain syndrome. DESIGN Single-blind, randomized, controlled noninferiority trial. SETTING University campus. PARTICIPANTS Forty elderly patients with myofascial pain syndrome completed the study. They were randomly allocated to SEIB (n = 22; mean age, 70.23 ± 6.11 years) or ultrasound (US) therapy (n = 18; mean age, 67.99 ± 5.64 years). INTERVENTION SEIB and US therapy (twice weekly for 4 consecutive weeks). OUTCOME MEASURES Visual analog scale (VAS), pressure pain threshold (PPT), and cervical lateral flexion (CLF) were measured at baseline and at 1, 2, 3, and 4 weeks. RESULTS The noninferiority test indicated that SEIB was not inferior to US for VAS, PPT, and CLF. Between-group comparisons showed no significant differences in the VAS (F = 2.579; p = 0.117), the PPT (F = 0.245; p = 0.624), and the CLF (F = 2.072; p = 0.159). In within-group comparisons, both groups presented significant differences in VAS (SEIB after 1 week and US after 1 week), PPT (SEIB after 3 weeks and US after 4 weeks), and CLF (SEIB after 4 weeks and US after 4 weeks) compared with baseline values. CONCLUSIONS SEIB for 4 weeks has an effect similar to that of US for desensitizing myofascial pain and increasing joint flexibility. High accessibility and low cost would make SEIB a practical self-treatment method in elderly patients with myofascial pain syndrome.
Why alcoholism is a disease.

Arguments of proponents and critics of a disease concept of alcoholism are reviewed. It is concluded that the disease concept of alcoholism is in accord with modern usage of the concept of disease in the philosophy of science and the practice of biomedical science. Ascription of the term "disease" involves a value judgment by experts that observed lawfully recurring signs and symptoms are a significant deviation from a norm or standard of health. Value judgments of this and other kinds are inherent in biobehavioral science and its application. Criticisms of the traditional conception of the disease concept fail to distinguish empirical questions of etiology, treatment, and the characteristic features of alcoholism from the conventional and evaluative nature of the classification "disease. " A critical review of the empirical research purporting to question the signs and symptoms of loss of control in alcoholics is also provided.
Delinquency in Society: The Essentials

Delinquency in Society: The Essentials is a concise introduction to the important topics covered by the same authors in the popular Delinquency in Society, Eighth Edition. This practical text explores how juvenile delinquency is defined, measured, and explained, as well as how the juvenile justice system deals with delinquent youth. This new Essentials text provides separate chapters focusing on the police, juvenile courts, corrections, and delinquency prevention.