Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiplexed gene transfer to a human T‐cell line by combining Sleeping Beauty transposon system with methotrexate selection

Engineered human T‐cells are a promising therapeutic modality for cancer immunotherapy. T‐cells expressing chimeric antigen receptors combined with additional genes to enhance T‐cell proliferation, survival, or tumor targeting may further improve efficacy but require multiple stable gene transfer events. Methods are therefore needed to increase production efficiency for multiplexed engineered cells. In this work, we demonstrate multiplexed, non‐viral gene transfer to a human T‐cell line with efficient selection (∼50%) of cells expressing up to three recombinant open reading frames. The efficient introduction of multiple genes to T‐cells was achieved using the Sleeping Beauty transposon system delivered in minicircles by nucleofection. We demonstrate rapid selection for engineered cells using methotrexate (MTX) and a mutant human dihydrofolate reductase resistant to methotrexate‐induced metabolic inhibition. Preferential amplification of cells expressing multiple transgenes was achieved by two successive rounds of increasing MTX concentration. This non‐viral gene transfer method with MTX step selection can potentially be used in the generation of clinical‐grade T‐cells housing multiplexed genetic modifications. Biotechnol. Bioeng. 2015;112: 1429–1436. © 2015 Wiley Periodicals, Inc.
Progress in laboratory based X-ray microscopy

In recent years X-ray tomography has made progressive steps towards spatial resolution in the sub-micron range. A limiting factor is the finite focal spot size of state-of-the-art microfocus tubes. In this contribution we present a radiography setup with an X-ray source capable of generation focal spot sizes down to 80 nm, thanks to special targets designed using Monte Carlo simulations. Together with a high geometric magnification and a low-noise photon-counting detector this makes the setup ideal for material characterisation at the nanoscale.
Isolation of cDNAs encoding 6‐phosphogluconate dehydrogenase and glucose‐6‐phosphate dehydrogenase from the mediterranean fruit fly Ceratitis capitata: correlating genetic and physical maps of chromosome 5

We have isolated and determined the nucleotide sequences for cDNA clones encoding glucose‐6‐phosphate dehydrogenase (G6PD) and 6‐phosphogluconate dehydrogenase (6PGD) from the medfly Ceratitis capitata. The derived amino acid sequences for G6PD and 6PGD are presented and compared with G6PDs and 6PGDs from other species. The codon usage of the cDNA clones has little bias with the notable exceptions of arginine, glycine and leucine.
Conditions for optimality of Naïve quantized finite horizon control

This paper presents properties of a control law which quantizes the unconstrained solution to a unitary horizon quadratic programme. This naïve quantized control law underlies many popular algorithms, such as ΣΔ-converters and decision feedback equalities, and is easily shown to be globally optimal for horizon one. However, the question arises as to whether it is also globally optimal for horizons greater than one, i.e. whether it solves a finite horizon quadratic programme, where decision variables are restricted to belonging to a quantized set. By using dynamic programming, we develop sufficient conditions for this to hold. The present analysis is restricted to first order plants. However, this case already raises a number of highly non-trivial issues. The results can be applied to arbitrary horizons and quantized sets, which may contain a finite or an infinite (though countable) number of elements.
Methicillin-Resistant Staphylococcus aureus Infection and Colonization Among Hospitalized Prisoners

We assessed methicillin-resistant Staphylococcus aureus (MRSA) infection and colonization in hospitalized prisoners. Of 434 admission surveillance cultures, 58 (13%) were positive for MRSA. The sensitivity of admission surveillance cultures of samples from the anterior nares was 72% and increased to 84% when the calculation included cultures of wound samples. Hospitalized prisoners are at high risk for MRSA infection and colonization, and surveillance should include cultures of nares and wound samples.
Accurate mass searching of individual lipid species candidates from high-resolution mass spectra for shotgun lipidomics.

RATIONALE With the increased mass accuracy and resolution in commercialized mass spectrometers, new developments on shotgun lipidomics could be expected with increased speed, dynamic range, and coverage over lipid species and classes. However, we found that the major issue by using high mass accuracy/resolution instruments to search lipid species is the partial overlap between the two-(13) C-atom-containing isotopologue of a species M (i.e., M+2 isotopologue) and the ion of a species with one less double bond than M (assigned here as L). This partial overlap alone could cause a mass shift of the species L to the lower mass end up to 12 ppm around m/z 750 as well as significant peak broadening. METHODS We developed an approach for accurate mass searching by exploring one of the major features of shotgun lipidomics data that lipid species of a class are present in ion clusters where neighboring masses from different species differ by one or a few double bonds. In the approach, a mass-searching window of 18 ppm (from -15 to 3 ppm) was first searched for an entire group of species of a lipid class. Then accurate mass searching of the plus one (13)C isotopologue of individual species was used to eliminate the potential false positive. RESULTS The approach was extensively validated through comparing with the species determined by the multi-dimensional MS-based shotgun lipidomics platform. The newly developed strategy of accurate mass searching enables the overlapped L species to be identified and the corresponding peak intensities to be acquired. CONCLUSIONS We believe that this novel approach could substantially broaden the applications of high mass accurate/resolution mass spectrometry for shotgun lipidomics.
Poly(D, L-lactide-co-glycolide) nanoparticles as delivery agents for photodynamic therapy: enhancing singlet oxygen release and photototoxicity by surface PEG coating

Poly(D, L-lactide-co-glycolide) (PLGA) nanoparticles (NPs) are being considered as nanodelivery systems for photodynamic therapy. The physico-chemical and biological aspects of their use remain largely unknown. Herein we report the results of a study of PLGA NPs for the delivery of the model hydrophobic photosensitizer ZnTPP to HeLa cells. ZnTPP was encapsulated in PLGA with high efficiency and the NPs showed negative zeta potentials and diameters close to 110 nm. Poly(ethylene glycol) (PEG) coating, introduced to prevent opsonization and clearance by macrophages, decreased the size and zeta potential of the NPs by roughly a factor of two and improved their stability in the presence of serum proteins. Photophysical studies revealed two and three populations of ZnTPP and singlet oxygen in uncoated and PEGylated NPs, respectively. Singlet oxygen is confined within the NPs in bare PLGA while it is more easily released into the external medium after PEG coating, which contributes to a higher photocytotoxicity towards HeLa cells in vitro. PLGA NPs are internalized by endocytosis, deliver their cargo to lysosomes and induce cell death by apoptosis upon exposure to light. In conclusion, PLGA NPs coated with PEG show high potential as delivery systems for photodynamic applications.
Basic Residues of the Helix Six Domain of Influenza Virus M1 Involved in Nuclear Translocation of M1 Can Be Replaced by PTAP and YPDL Late Assembly Domain Motifs

ABSTRACT Influenza type A virus matrix (M1) protein possesses multiple functional motifs in the helix 6 (H6) domain (amino acids 91 to 105), including nuclear localization signal (NLS) (101-RKLKR-105) involved in translocating M1 from the cytoplasm into the nucleus. To determine the role of the NLS motif in the influenza virus life cycle, we mutated these and the neighboring sequences by site-directed mutagenesis, and influenza virus mutants were generated by reverse genetics. Our results show that infectious viruses were rescued by reverse genetics from all single alanine mutations of amino acids in the H6 domain and the neighboring region except in three positions (K104A and R105A within the NLS motif and E106A in loop 6 outside the NLS motif). Among the rescued mutant viruses, R101A and R105K exhibited reduced growth and small-plaque morphology, and all other mutant viruses showed the wild-type phenotype. On the other hand, three single mutations (K104A, K105A, and E106A) and three double mutations (R101A/K102A, K104A/K105A, and K102A/R105A) failed to generate infectious virus. Deletion (ΔYRKL) or mutation (4A) of YRKL also abolished generation of infectious virus. However, replacement of the YRKL motif with PTAP or YPDL as well as insertion of PTAP after 4A mutation yielded infectious viruses with the wild-type phenotype. Furthermore, mutant M1 proteins (R101A/K102A, ΔYRKL, 4A, PTAP, 4A+PTAP, and YPDL) when expressed alone from cloned cDNAs were only cytoplasmic, whereas the wild-type M1 expressed alone was both nuclear and cytoplasmic as expected. These results show that the nuclear translocation function provided by the positively charged residues within the NLS motif does not play a critical role in influenza virus replication. Furthermore, these sequences of H6 domain can be replaced by late (L) domain motifs and therefore may provide a function similar to that of the L domains of other negative-strand RNA and retroviruses.
Combined Refrigerant Volume Control Through An Electronic Expansion Valve With the Self-Tuning Fuzzy Algorithm Applied

This paper gives a study of how to carry out a combined refrigerant volume control using an electronic expansion valve (EEV) and the specific measures to apply selftuning fuzzy algorithm to refrigeration control system. The simulation analysis on the superheat fuzzy controller was completed by Simulink. Different scale factors and weight factors were employed during the process, and their effects on the controller were concluded, Based the self-tuning fuzzy controller was developed by changing these factors on line through some algorithms. The combined refrigerant volume control method through the EEV was proposed, and its validation was verified by experiments.
Sonographic diagnosis of biliary atresia in pediatric patients using the "triangular cord" sign versus gallbladder length and contraction.

OBJECTIVE A retrospective review was performed to evaluate the importance of the "triangular cord" sign in comparison with gallbladder length and contraction for the diagnosis of biliary atresia in pediatric patients. MATERIALS AND METHODS Fifty-five fasting infants with cholestatic jaundice were examined on sonography. The examinations focused on the visualization of the triangular cord sign and assessment of gallbladder length and contraction. The diagnosis of neonatal hepatitis or of other causes of infantile cholestasis was made if symptom resolution occurred during follow-up. RESULTS A triangular cord sign was found in 27 of 29 infants with biliary atresia and in one of 26 infants with neonatal hepatitis or other causes of infantile cholestasis. The diagnostic accuracy was 95%, sensitivity was 93%, and specificity was 96%. The gallbladder was thought to be abnormal if it was less than 1.5 cm long, was not detectable, or was detectable but had no lumen. The gallbladder was abnormal in 21 of 29 infants with biliary atresia, whereas it was abnormal in eight of 26 infants with neonatal hepatitis or other causes of infantile cholestasis. The diagnostic accuracy was 71%, sensitivity was 72%, and specificity was 69%. The gallbladder was detectable on sonography in 13 infants with biliary atresia and 26 infants with neonatal hepatitis or other causes of infantile cholestasis. Gallbladder contraction was not confirmed in 11 of 13 infants with biliary atresia and seven of 26 infants with neonatal hepatitis or other causes of infantile cholestasis. The diagnostic accuracy was 77%, sensitivity was 85%, and specificity was 73%. CONCLUSION The triangular cord sign was a more useful sonographic finding for diagnosing biliary atresia than gallbladder length and contraction.
Solution Structure of Porcine Delta Sleep-inducing Peptide Immunoreactive Peptide A Homolog of the ShortsightedGene Product*

The 77-residue delta sleep-inducing peptide immunoreactive peptide (DIP) is a close homolog of the Drosophila melanogaster shortsighted gene product. Porcine DIP (pDIP) and a peptide containing a leucine zipper-related partial sequence of pDIP, pDIP(9–46), was synthesized and studied by circular dichroism and nuclear magnetic resonance spectroscopy in combination with molecular dynamics calculations. Ultracentrifugation, size exclusion chromatography, and model calculations indicated that pDIP forms a dimer. This was confirmed by the observation of concentration-dependent thermal folding-unfolding transitions. From CD spectroscopy and thermal folding-unfolding transitions of pDIP(9–46), it was concluded that the dimerization of pDIP is a result of interaction between helical structures localized in the leucine zipper motif. The three-dimensional structure of the protein was determined with a modified simulated annealing protocol using experimental data derived from nuclear magnetic resonance spectra and a modeling approach based on an established strategy for coiled coil structures. The left-handed super helical structure of the leucine zipper type sequence resulting from the modeling approach is in agreement with known leucine zipper structures. In addition to the hydrophobic interactions between the amino acids at the heptade positions a and d, the structure of pDIP is stabilized by the formation of interhelical i to i′ + 5 salt bridges. This result was confirmed by the pH dependence of the thermal-folding transitions. In addition to the amphipatic helix of the leucine zipper, a second helix is formed in the NH2-terminal part of pDIP. This helix exhibits more 310-helix character and is less stable than the leucine zipper helix. For the COOH-terminal region of pDIP no elements of regular secondary structure were observed.
Impact analysis of application layer DDoS attacks on web services: a simulation study

Due to a wide range of attacks possible on the internet, abundance of security solutions exists in the market today. In spite of this, distributed denial of service (DDoS) attack is still considered irrepressible, as none of the present-day solutions seems to completely eradicate its existence. The most sophisticated form of this attack, application-layer DDoS attack, is on the rise seeking to its surging frequency in recent years. With a primary focus on their detection and mitigation, the researchers have made significant contributions toward the related literature. We begin with introducing application-layer DDoS attacks followed by an analysis of the recent contributions in a nutshell. Subsequently, the underlying mechanism behind the application-layer DDoS attacks is discussed to apprehend its effect on traditional web server architecture. Finally, two independent exhaustive simulations are carried out to evaluate the impact of such attacks on the performance of a web server from multiple perspectives. Multifarious experimental designs corresponding to different attack intensities and server performance parameters are exercised during our first simulation scenario in order to report diverse possible scenarios. The second simulation scenario examines three well-known application-layer DDoS attack strategies that an attacker usually adopts in order to instigate an application-layer DDoS attack.
Experimental anti‐angiogenesis causes upregulation of genes associated with poor survival in glioblastoma

Vascular endothelial growth factor (VEGF) inhibitors are the most promising anti‐angiogenic agents used increasingly in the clinic. However, to be efficient, anti‐VEGF agents need to be associated with classic chemotherapy. Exploring gene regulation in tumor cells during anti‐angiogenesis might help to comprehend the molecular basis of response to treatment. To generate a defined anti‐angiogenic condition in vivo, we transfected human glioma cells with short‐interfering RNAs against VEGF‐A and implanted them on the chick chorio‐allantoic membrane. Gene regulation in avascular tumors was studied using human Affymetrix™ GeneChips. Potentially important genes were further studied in glioma patients. Despite strong VEGF inhibition, we observed recurrent formation of small, avascular tumors. CHI3L2, IL1B, PI3/elafin and CHI3L1, which encodes for YKL‐40, a putative prognosticator for various diseases, including cancer, were strongly up‐regulated in avascular glioma. In glioblastoma patients, these genes showed coregulation and their expression differed significantly from low‐grade glioma. Importantly, high levels of CHI3L1 (p = 0.036) and PI3/elafin mRNA (p = 0.0004) were significantly correlated with poor survival. Cox regression analysis further confirmed that PI3 and CHI3L1 levels are survival markers independent from patient age and sex. Elafin‐positive tumor cells were only found in glioblastoma, where they were clustered around necrotic areas. PI3/elafin is strongly induced by serum deprivation and hypoxia in U87 glioma cells in vitro. Our results indicate that anti‐angiogenesis in experimental glioma drives expression of critical genes which relate to disease aggressiveness in glioblastoma patients. In particular, CHI3L1 and PI3/elafin may be useful as new prognostic markers and new therapeutic targets. © 2007 Wiley‐Liss, Inc.
Modelisation des effets du bilan hydrique sur la production primaire et la croissance d'un couvert de pin maritime (pinus pinaster ait) en lande humide

Le pin maritime (pinus pinaster ait. ) est la premiere espece forestiere francaise en terme de surface boisee. Son importance economique et les questions concernant la durabilite d'un tel ecosysteme cultive l'ont place au centre d'etudes visant a comprendre son fonctionnement. Dans les landes, sa croissance est limitee par la disponibilite en eau et mineraux. Nous avons cherche, a l'aide d'un modele, a caracteriser les effets du bilan hydrique du peuplement sur l'assimilation et la croissance des arbres. Nous avons d'abord presente les mesures de biomasse realisees sur des pins de 5,20 et 26 ans. Les relations allometriques obtenues permettent d'estimer les biomasses de l'arbre par compartiment grace au diametre a 1. 30 m (dbh) et a l'age du pin. Cela fournit des outils de qualite satisfaisante, pratiques a appliquer a grande echelle. Le modele de production primaire du peuplement couple un bilan hydrique (loustau et al. 1997) a un schema de transformation de l'energie lumineuse en carbone fixe, a l'aide d'une efficience lumineuse sensible aux conditions hydriques. La croissance annuelle en biomasse, dbh et hauteur des arbres du peuplement est basee sur les relations allometriques elaborees precedemment. La comparaison a un modele theorique montre que le jeu de donnees de parametrage actuel de l'efficience manque de conditions hydriques tres seches, et l'efficience ne presente qu'une faible sensibilite aux variations inter-annuelles d'alimentation en eau. La prise en compte de la secheresse permet au contraire de reproduire de maniere satisfaisante les variations de croissance en diametre observees. Les relations carbone- eau ont aussi ete abordees au travers du signal isotopique du carbone mesure sur la cellulose extraite des cernes. Discrimination et efficience de l'eau integree calculee avec le modele ne montrent pas de relation lineaire marquee, mais leurs evolutions annuelles fluctuent en parallele, confirmant l'existence d'un lien entre les deux processus.
The impact of a sibling's life‐limiting genetic condition on adult brothers and sisters

It is estimated that rare diseases affect the lives of over three million people in the United Kingdom. Of these, a significant proportion are children and young people with genetic life‐limiting or life‐shortening conditions. This study used a qualitative approach with in‐depth semi‐structured interviews to explore the experiences of 10 adult siblings of a baby diagnosed with Trisomy 13 (Patau syndrome) or Trisomy 18 (Edward syndrome). Findings illustrate that parental grief from the time of their child's diagnosis onward is also experienced by siblings. Although young adults may have conflicting feelings as a bereaved sibling, there is evidence that the experience impacts on their world views and their attitudes about prospective and expectant parenthood. The study highlights the importance of providing siblings with short‐term and long‐term support from the time of their brother's or their sister's diagnosis onward and provides new understanding about benefit of professional and peer support in helping young adults develop resilience and coping strategies.
A Block Nonlocal TV Method for Image Restoration

In this paper, we propose a block nonlocal total variation (TV) regularization method for image restoration. We extend the existing nonlocal TV method in two aspects: first, some block nonlocal operators are introduced to extend the point-based nonlocal diffusion as a block-based nonlocal diffusion process; second, the weighting function in the nonlocal method can be adaptively determined by the cost functional itself. The proposed method is derived from a block-based maximum a posteriori estimation. By the assumption of the self-similarity of small patches, we formulate a regularization term as a log-likelihood functional of a mixture model. To optimize this regularization term efficiently, we employ the idea of the expectation maximum algorithm and give a variational framework to propose a block-based nonlocal TV regularization. The weighting function occurring in our model can be regarded as a probability of the similarity for image patches, and it can be updated adaptively according to the newest esti.
Efficient cell migration requires global chromatin condensation

Cell migration is a fundamental process that is necessary for the development and survival of multicellular organisms. Here, we show that cell migration is contingent on global condensation of the chromatin fiber. Induction of directed cell migration by the scratch-wound assay leads to decreased DNaseI sensitivity, alterations in the chromatin binding of architectural proteins and elevated levels of H4K20me1, H3K27me3 and methylated DNA. All these global changes are indicative of increased chromatin condensation in response to induction of directed cell migration. Conversely, chromatin decondensation inhibited the rate of cell migration, in a transcription-independent manner. We suggest that global chromatin condensation facilitates nuclear movement and reshaping, which are important for cell migration. Our results support a role for the chromatin fiber that is distinct from its known functions in genetic processes.