Miracle-dz/UniFAR-FTUs huggingface dataset:
Engineering Mammalian Mucin-type O-Glycosylation in Plants*

Background: Plants lack mammalian GalNAc-type protein O-glycosylation. Results: Transient expression of a Glc(NAc) C4-epimerase and a polypeptide GalNAc-transferase in Nicotiana benthamiana resulted in O-glycosylation. Conclusion: Mammalian O-glycosylation can be established in plants. Significance: Plants may serve as host cells for recombinant production of custom-designed O-glycoproteins. Mucin-type O-glycosylation is an important post-translational modification that confers a variety of biological properties and functions to proteins. This post-translational modification has a particularly complex and differentially regulated biosynthesis rendering prediction and control of where O-glycans are attached to proteins, and which structures are formed, difficult. Because plants are devoid of GalNAc-type O-glycosylation, we have assessed requirements for establishing human GalNAc O-glycosylation de novo in plants with the aim of developing cell systems with custom-designed O-glycosylation capacity. Transient expression of a Pseudomonas aeruginosa Glc(NAc) C4-epimerase and a human polypeptide GalNAc-transferase in leaves of Nicotiana benthamiana resulted in GalNAc O-glycosylation of co-expressed human O-glycoprotein substrates. A chimeric YFP construct containing a 3.5 tandem repeat sequence of MUC1 was glycosylated with up to three and five GalNAc residues when co-expressed with GalNAc-T2 and a combination of GalNAc-T2 and GalNAc-T4, respectively, as determined by mass spectrometry. O-Glycosylation was furthermore demonstrated on a tandem repeat of MUC16 and interferon α2b. In plants, prolines in certain classes of proteins are hydroxylated and further substituted with plant-specific O-glycosylation; unsubstituted hydroxyprolines were identified in our MUC1 construct. In summary, this study demonstrates that mammalian type O-glycosylation can be established in plants and that plants may serve as a host cell for production of recombinant O-glycoproteins with custom-designed O-glycosylation. The observed hydroxyproline modifications, however, call for additional future engineering efforts.
An Embedded Closed-Loop Fault-Tolerant Control Scheme for Nonredundant VSI-Fed Induction Motor Drives

The nonredundant voltage-source inverter, which exploits the possibility of minimum additional components for reconfiguration and operation, is a promising solution to manage faults in one inverter leg. However, control schemes at prefault and postfault conditions are always designed, separately making it hard for control scheme adaptation from normal to fault tolerant. In order to achieve smooth transitions from prefault to postfault, an embeddable fault-tolerant method based on predictive torque control (PTC) is proposed. A generalized voltage vectors, switching command, and cost function accounting for both healthy and faulty conditions are introduced to carry out a general control scheme. A novel fault-diagnosis method based on probability density analysis of the sampling currents is presented for open-circuit fault isolation under PTC scheme. Seamless likely and rapid transient processes from fault occurrence to postfault operation are achieved. Experimental results have demonstrated that the proposed scheme can make power switch fault easily managed by the controller itself.
Economic foundations of morality: Questions of transparency and ethics in Russian journalism

Th is study examines the questions of ethics and transparency in Russian journalism. Th e paper explains instances of non-transparent behavior among Russian journalists in light of economic hardship that Russian journalists in the province face in their everyday life. Specifi cally, this study attempts to explicate the connection between transparency, journalism ethics, and economic and social conditions in which regional journalists function in Russia. Th is paper argues that morality may depend on economic conditions of an individual and poor economic conditions tend to diminish human dignity. In turn, diminished human dignity more readily puts in jeopardy professional ethical principles and contributes to non-transparent media practices. Poor economic conditions have implications for regional journalism practice in Russia, where they create a vicious circle which Russian journalists fail to break.
Refractive state following retinal reattachment and silicone oil tamponade in dogs.

OBJECTIVE To evaluate the refractive error induced by intraocular administration of silicone oil (SiO) in dogs. ANIMALS 47 client-owned dogs evaluated for blindness secondary to retinal detachment. PROCEDURES -3-port pars plana vitrectomy with perfluoro-octane and SiO exchange (1,000- or 5,000-centistoke SiO) was performed in 1 or both eyes for all dogs (n = 63 eyes), depending on which eye or eyes were affected. Dogs were normotensive, had complete oil filling of the eyes, and were examined in a standing position for retinoscopic examination of both eyes (including healthy eyes). RESULTS The mean refractive error for SiO-filled phakic and pseudophakic eyes was 2.67 and 3.24 D, respectively. The mean refractive error for SiO-filled aphakic eyes was 6.50 D. Dogs in which 5,000-centistoke SiO was used had consistently greater positive refractive errors (mean, 3.45 D), compared with dogs in which 1,000-centistoke SiO was used (mean, 2.10 D); however, the difference was nonsignificant. There was no significant linear relationship between refractive error and the number of days between surgery and retinoscopy. CONCLUSIONS AND CLINICAL RELEVANCE Hyperopia was observed in all dogs that underwent SiO tamponade, regardless of lens status (phakic, pseudophakic, or aphakic). Aphakic eyes underwent a myopic shift when filled with SiO. Pseudophakic eyes appeared to be more hyperopic than phakic eyes when filled with SiO; however, additional investigation is needed to confirm the study findings.
Long-term functional outcomes after radical cystectomy with ileal bladder substitute: does the definition of continence matter?

Abstract Objective: Functional outcomes after ileal bladder substitution reflect the expectations of future patients at a particular centre. The aim of this study was to use validated questionnaires and a pad-weighing test to investigate functional outcomes after neobladder reconstruction at long-term follow-up in patients at a single centre. Materials and methods: During 2005 − 2015, 75 patients received a Studer ileal bladder substitute at the Department of Urology, Malmö. Forty-six of these patients were alive for follow-up and were evaluated using the pad-weighing test and the International Consultation on Incontinence Questionnaire–Urinary Incontinence Short Form (ICIQ-UI-SF), the Female Sexual Function Index (FSFI) and the International Index of Erectile Function (IIEF). Results: Five of 37 evaluable patients (14%) were considered fully continent, reporting a pad-weighing test result of 0 g and an ICIQ-UI-SF score of 0. The median ICIQ-UI-SF score was 8 [interquartile range (IQR) 3–11], and seven patients (17%) were continent according to the ICIQ-UI-SF score only. In the pad-weighing test, 28 out of 37 patients (76%) reported 0 g day-time leakage whereas only 12 out of 37 patients (32%) reported 0 g night-time leakage. At follow-up, nine out of 39 (23%) of evaluable male patients were potent. The median ICIQ-UI-SF score was significantly lower during the second half of the study period [4 (IQR 0–8) vs 10 (IQR 6–14); p = . 003]. The inverse applied to the median IIEF score [5 (IQR 3–12) vs 2 (IQR 1–4); p = . 02]. Conclusions: Functional outcomes at long-term follow-up after radical cystectomy and Studer ileal bladder substitute were at best modest in this series. Better outcomes during the second half of the study period might be explained by improved patient selection and a refined surgical technique, but possibly also by longer follow-up of patients during the first half of the period resulting in a more pronounced time-dependent decline in functional outcomes.
Electrical Properties of Ge pMOSFETs With Ultrathin EOT HfO2/AlOx/GeOx Gate-Stacks and NiGe Metal Source/Drain

The high performance Ge pMOSFETs have been realized with ultrathin HfO<sub>2</sub>/AlO<sub><italic>x</italic></sub>/GeO<sub><italic>x</italic></sub>/Ge gate-stacks fabricated by ozone postoxidation (OPO) and NiGe metal source/drain (S/D). It is found that OPO yields a reduction of interface traps and an improvement of dielectric strength for the HfO<sub>2</sub>/AlO<sub><italic>x</italic></sub>/GeO<sub><italic>x</italic></sub>/Ge gate-stacks. On the other hand, it is also confirmed that the NiGe metal S/D structure decreases the S/D parasitic resistance severely. As a result, the record high drive current has been realized under a comparable gate length for present Ge pMOSFET structure with the ultrathin equivalent oxide thickness HfO<sub>2</sub>/AlO<sub><italic>x</italic></sub>/GeO<sub><italic>x</italic></sub>/Ge gate-stack and the low parasitic resistance NiGe S/D.
La Crosse virions contain a primer-stimulated RNA polymerase and a methylated cap-dependent endonuclease

Purified La Crosse virions in vitro were found to transcribe their negative polarity (-)RNA genomes. This polymerase activity was stimulated by oligonucleotides such as (A)nG, cap analogs such as m7GpppAm, and natural mRNAs such as alfalfa mosaic virus RNA 4. For (A)nG- and alfalfa mosaic virus RNA 4-stimulated reactions, evidence is presented that these RNAs stimulate activity by acting as primers for viral transcription. The cap analogs appear to stimulate activity via an alternative mechanism. Purified La Crosse virions were also found to contain an endonuclease which specifically cleaves alfalfa mosaic virus RNA 4 when this RNA contains a methylated cap group.
Changing Practice: Research on the Impact of Continuing Professional Development in Higher Education

• In higher education, we still have much to learn about the nature of teacher thinking, about the construction of curricula, and about how teachers become reflective about their practice. Eraut (1994) emphasised that professionals continually learn on the job but that unless time is set aside to deliberate, the learning may not be integrated into any general theory of practice. Also, it is argued in the most recent literature (Day & Sachs 2004) that there is a gap in our knowledge of the effects of CPD upon the thinking, planning and practice of individual teachers. Kelchtermans (2004) highlights the need to answer the key question as to what kind of professionalism continuous professional development should contribute and the discussion is set in the wider context of the debate about the professionalism of the academic community in these changed times. • The aim of this paper is to explore important issues in relation to the professional development of the academic community through the detailing of a research study which measured the impact on the teaching practice of lecturers who have graduated from the Postgraduate Certificate in Third Level Learning and Teaching Course over a period extending from 2000-2003. A qualitative questionnaire was distributed to the forty five successful graduates of the course to establish the impact the course had made on these lecturers’ professional practice. • 25 lecturers returned completed questionnaires; all indicated that impact had been made on their teaching practice, and a number of changes had taken place. The most significant of these had been increased reflection on current teaching practice; the introduction of new teaching strategies; increased focus on the design and delivery of classes; more work taking place on course teams; an increased in confidence about learning and teaching and a more student-centred approach taken to teaching. Abstract
Experimental modeling of breast cancer detection by using radar aids

Breast cancer is one of the most common types of cancer among women. Due to this fact, providing methods to assess the early-stage diagnosis and treatment of the breast cancer is of a great interest for researchers in the last decades. The article describes in detail the experiment of imaging breast tumors using radar aids. The development of microwave breast cancer detection and treatment techniques has been driven by reports of substantial contrast in the dielectric properties of malignant and normal breast tissues. During the experiment, two different phantoms of breast were used: one without the dielectric inclusions, another with dielectric inclusions mimicking malignancy of the breast tissue. The materials of the phantoms were selected in such a way as to its dielectric properties were same the dielectric properties of biological tissues of the breast. During the experiments a vector network analyzer (Rohde&Schwarz) with a single helical antenna attached was used for measuring of S11 parameters. The antenna was pointed to the phantom behind which radio absorbing material was placed to reduce the clutter. Mechanical scanner controlled by Seeduino was used to move the phantom. We conducted measurements at frequencies from 5.6 to 6.6 GHz, 14 to 15 GHz and from 21 to 22 GHz with a step of 0.2 GHz. Obtained images were processed by using software “RASCAN-Q”. It was shown that the applied method allows to detect dielectric inhomogeneities in biological tissues. The results, published in the article, have been obtained in the framework of the implementation of the project part of the Russian Foundation for Basic Research (grant No. 26 16-37-00276\16).
Specificity of light and electron microscopic features of hypertrophic obstructive and nonobstructive cardiomyopathy. Qualitative, quantitative and etiologic aspects.

A review is presented of the histologic and ultrastructural abnormalities found in the hearts of patients with hypertrophic cardiomyopathy. Evidence is presented to show that myocardial fiber disarray is found in hypertrophic cardiomyopathy as well as in other conditions; however, in the latter it seldom involves more than 5% of the myocytes in transverse sections of ventricular septum. A new theory of morphogenesis is proposed to account for the asymmetric cardiac hypertrophy that characterizes hypertrophic cardiomyopathy. This theory is summarized as follows: (1) hypercontractility is the underlying abnormality affecting cardiac myocytes; (2) this hypercontractility is present during embryonic development and constitutes the stimulus to the inappropriate increase in cardiac mass that takes place in hypertrophic cardiomyopathy; (3) during embryonic development this stimulus results in increased mitotic division (i.e. hyperplasia) rather than in increased size of individual myocytes (i.e. hypertrophy); (4) hyperplasia is preferentially increased in the ventricular septum (perhaps because of the mechanical forces exerted by left and right ventricular contraction on the ventricular septum), thus exaggerating the asymmetric growth that occurs normally in this area during prenatal development; (5) after birth, the septal asymmetry does not regress in patients with hypertrophic cardiomyopathy, as it does in normal individuals, because it is complicated by hyperplasia (i.e. increased numbers of myocytes are already present in the ventricular septum); (6) the prenatal phase of hyperplasia is followed by a postnatal phase of gradual, progressive hypertrophy in which myocytes enlarge, septal hypertrophy becomes exaggerated, and clinical symptoms eventually develop.
Overproduction of the beta subunit of DNA polymerase III holoenzyme reduces UV mutagenesis in Escherichia coli

Overproduction of the beta subunit of DNA polymerase III holoenzyme caused a 5- to 10-fold reduction of UV mutagenesis along with a slight increase in sensitivity to UV light in Escherichia coli. The same effects were observed in excision-deficient cells, excluding the possibility that they were mediated via changes in excision repair. In contrast, overproduction of the alpha subunit of the polymerase did not influence either UV mutagenesis or UV sensitivity. The presence of the mutagenesis proteins MucA and MucB expressed from a plasmid alleviated the effect of overproduced beta on UV mutagenesis. We have previously suggested that DNA polymerase III holoenzyme can exist in two forms: beta-rich form unable to bypass UV lesions and a beta-poor form capable of bypassing UV lesions (O. Shavitt and Z. Livneh, J. Biol. Chem. 264:11275-11281, 1989). The beta-poor form may be related to an SOS form of DNA polymerase III designed to perform translesion polymerization under SOS conditions and thereby generate mutations. On the basis of this model, we propose that the overproduced beta subunit affects the relative abundance of the regular replicative beta-rich polymerase and the SOS bypass-proficient polymerase by sequestering the polymerase molecules to the beta-rich form and blocking the SOS form.
Cathepsin D regulates cathepsin B activation and disease severity predominantly in inflammatory cells during experimental pancreatitis

Acute pancreatitis is a complex disorder involving both premature intracellular protease activation and inflammatory cell invasion. An initiating event is the intracellular activation of trypsinogen by cathepsin B (CTSB), which can be induced directly via G protein–coupled receptors on acinar cells or through inflammatory cells. Here, we studied CTSB regulation by another lysosomal hydrolase, cathepsin D (CTSD), using mice with a complete (CTSD−/−) or pancreas-specific conditional CTSD knockout (KO) (CTSDf/f/p48Cre/+). We induced acute pancreatitis by repeated caerulein injections and isolated acinar and bone marrow cells for ex vivo studies. Supramaximal caerulein stimulation induced subcellular redistribution of CTSD from the lysosomal to the zymogen-containing subcellular compartment of acinar cells and activation of CTSD, CTSB, and trypsinogen. Of note, the CTSD KO greatly reduced CTSB and trypsinogen activation in acinar cells, and CTSD directly activated CTSB but not trypsinogen in vitro. During pancreatitis in pancreas-specific CTSDf/f/p48Cre/+ animals, markers of severity were reduced only at 1 h, whereas in the complete KO, this effect also included the late disease phase (8 h), indicating an important effect of extra-acinar CTSD on course of the disease. CTSD−/− leukocytes exhibited reduced cytokine release after lipopolysaccharide (LPS) stimulation, and CTSD KO also reduced caspase-3 activation and apoptosis in acinar cells stimulated with the intestinal hormone cholecystokinin. In summary, CTSD is expressed in pancreatic acinar and inflammatory cells, undergoes subcellular redistribution and activation during experimental pancreatitis, and regulates disease severity by potently activating CTSB. Its impact is only minimal and transient in the early, acinar cell–dependent phase of pancreatitis and much greater in the later, inflammatory cell–dependent phase of the disease.
Importance of apoptosis in the histopathology of drug related lesions in the large intestine.

AIM: To investigate the possibility that the incidence of apoptotic bodies in the cryptal epithelium might help to identify colonic lesions due to drugs, especially non-steroidal anti-inflammatory drugs (NSAIDs). METHODS: The apoptotic count (AC) the number of apoptotic bodies per 100 crypts was calculated in a series of colorectal biopsy specimens, stained with haematoxylin and eosin from patients with (a) known or suspected drug induced colitis and (b) inflammatory bowel disease before or after treatment with salazopyrine or corticosteroids. These specimens were compared with normal biopsy specimens from a control group of comparable age and sex distribution. RESULTS: Under normal conditions apoptotic bodies were seldom seen at all and the mean apoptotic count was less than 1.0. In untreated inflammatory bowel disease the mean apoptotic count was marginally increased (2.4), but when there was a partial response to drug treatment the apoptotic count rose to 13.1 (p 0.003). In colonic lesions directly attributable to drugs the apoptotic count was always increased, reaching its highest level (106) with 5-fluorouracil. In colitis related to NSAIDs apoptoses were associated with inflammation, most notably an increase in lymphocytes in both lamina propria and epithelium. CONCLUSION: The presence of crypt apoptoses in substantial numbers (with an apoptotic count in excess of 5) should always raise the possibility of drug effect. The mechanisms involved are not clear but with NSAIDs the changes might well be immunologically mediated.
Distinct regulatory elements control muscle-specific, fiber-type-selective, and axially graded expression of a myosin light-chain gene in transgenic mice

The fast alkali myosin light chain 1f/3f (MLC1f/3f) gene is developmentally regulated, muscle specific, and preferentially expressed in fast-twitch fibers. A transgene containing an MLC1f promoter plus a downstream enhancer replicates this pattern of expression in transgenic mice. Unexpectedly, this transgene is also expressed in a striking (approximately 100-fold) rostrocaudal gradient in axial muscles (reviewed by J. R. Sanes, M. J. Donoghue, M. C. Wallace, and J. P. Merlie, Cold Spring Harbor Symp. Quant. Biol. 57:451-460, 1992). Here, we analyzed the expression of mutated transgenes to map sites necessary for muscle-specific, fiber-type-selective, and axially graded expression. We show that two E boxes (myogenic factor binding sites), a homeodomain (hox) protein binding site, and an MEF2 site, which are clustered in an approximately 170-bp core enhancer, are all necessary for maximal transgene activity in muscle but not for fiber-type- or position-dependent expression. A distinct region within the core enhancer promotes selective expression of the transgene in fast-twitch muscles. Sequences that flank the core enhancer are also necessary for high-level activity in transgenic mice but have little influence on activity in transfected cells, suggesting the presence of regions resembling matrix attachment sites. Truncations of the MLC1f promoter affected position-dependent expression of the transgene, revealing distinct regions that repress transgene activity in neck muscles and promote differential expression among intercostal muscles. Thus, the whole-body gradient of expression displayed by the complete transgene may reflect the integrated activities of discrete elements that regulate expression in subsets of muscles. Finally, we show that transgene activity is not significantly affected by deletion or overexpression of the myoD gene, suggesting that intermuscular differences in myogenic factor levels do not affect patterns of transgene expression. Together, our results provide evidence for at least nine distinct sites that exert major effects on the levels and patterns of MLC1f expression in adult muscles.