Miracle-dz/UniFAR-FTUs huggingface dataset:
Multilayered control of peroxisomal activity upon salt stress in Saccharomyces cerevisiae

Peroxisomes are dynamic organelles and the sole location for fatty acid β‐oxidation in yeast cells. Here, we report that peroxisomal function is crucial for the adaptation to salt stress, especially upon sugar limitation. Upon stress, multiple layers of control regulate the activity and the number of peroxisomes. Activated Hog1 MAP kinase triggers the induction of genes encoding enzymes for fatty acid activation, peroxisomal import and β‐oxidation through the Adr1 transcriptional activator, which transiently associates with genes encoding fatty acid metabolic enzymes in a stress‐ and Hog1‐dependent manner. Moreover, Na+ and Li+ stress increases the number of peroxisomes per cell in a Hog1‐independent manner, which depends instead of the retrograde pathway and the dynamin related GTPases Dnm1 and Vps1. The strong activation of the Faa1 fatty acyl‐CoA synthetase, which specifically localizes to lipid particles and peroxisomes, indicates that adaptation to salt stress requires the enhanced mobilization of fatty acids from internal lipid stores. Furthermore, the activation of mitochondrial respiration during stress depends on peroxisomes, mitochondrial acetyl‐carnitine uptake is essential for salt resistance and the number of peroxisomes attached to the mitochondrial network increases during salt adaptation, which altogether indicates that stress‐induced peroxisomal β‐oxidation triggers enhanced respiration upon salt shock.
Acinetobacter sp. isolates from emergency departments in two hospitals of South Korea.

A total of 114 Acinetobacter sp. isolates were collected from patients in the emergency departments (EDs) of two Korean hospitals. Most isolates belonged to the Acinetobacter baumannii complex (105 isolates, 92.1 %). Imipenem resistance was found in 39 isolates (34.2 %) of the Acinetobacter sp. isolates, and 6 colistin-resistant isolates were also identified. Species distribution and antimicrobial-resistance rates were different between the two hospitals. In addition, two main clones were identified in the imipenem-resistant A. baumannii isolates from hospital B, but very diverse and novel genotypes were found in those from hospital A. Many Acinetobacter sp. isolates, including the imipenem-resistant A. baumannii, are considered to be associated with the community. The evidence of high antimicrobial resistance and different features in these Acinetobacter sp. isolates between the two EDs suggests the need for continuous testing to monitor changes in epidemiology.
A combination of cis-2-decenoic acid and antibiotics eradicates pre-established catheter-associated biofilms.

The catheterized urinary tract provides ideal conditions for the development of biofilm populations. Catheter-associated urinary tract infections (CAUTIs) are recalcitrant to existing antimicrobial treatments; therefore, established biofilms are not eradicated completely after treatment and surviving biofilm cells will carry on the infection. Cis-2-decenoic acid (CDA), an unsaturated fatty acid, is capable of inhibiting biofilm formation by Pseudomonas aeruginosa and of inducing the dispersion of established biofilms by multiple types of micro-organisms. Here, the ability of CDA to induce dispersal in pre-established single- and dual-species biofilms formed by Escherichia coli and Klebsiella pneumoniae was measured by using both semi-batch and continuous cultures bioassays. Removal of the biofilms by combined CDA and antibiotics (ciprofloxacin or ampicillin) was evaluated using microtitre plate assays (crystal violet staining). The c.f. u. counts were determined to assess the potential of combined CDA treatments to kill and eradicate pre-established biofilms formed on catheters. The effects of combined CDA treatments on biofilm surface area and bacteria viability were evaluated using fluorescence microscopy, digital image analysis and live/dead staining. To investigate the ability of CDA to prevent biofilm formation, single and mixed cultures were grown in the presence and absence of CDA. Treatment of pre-established biofilms with only 310 nM CDA resulted in at least threefold increase in the number of planktonic cells in all cultures tested. Whilst none of the antibiotics alone exerted a significant effect on c.f. u. counts and percentage of surface area covered by the biofilms, combined CDA treatments led to at least a 78% reduction in biofilm biomass in all cases. Moreover, most of the biofilm cells remaining on the surface were killed by antibiotics. The addition of 310 nM CDA significantly prevented biofilm formation by the tested micro-organisms, even within mixed cultures, indicating the ability of CDA to inhibit biofilm formation by other types of bacteria in addition to Pseudomonas aeruginosa. These findings suggested that the biofilm-preventive characteristics of CDA make it a noble candidate for inhibition of biofilm-associated infections such as CAUTIs, which paves the way toward developing new strategies to control biofilms in clinical as well as industrial settings.
Stimulation of PgdA‐dependent peptidoglycan N‐deacetylation by GpsB‐PBP A1 in Listeria monocytogenes

Listeria monocytogenes and other pathogenic bacteria modify their peptidoglycan to protect it against enzymatic attack through the host innate immune system, such as the cell wall hydrolase lysozyme. During our studies on GpsB, a late cell division protein that controls activity of the bi‐functional penicillin binding protein PBP A1, we discovered that GpsB influences lysozyme resistance of L. monocytogenes as mutant strains lacking gpsB showed an increased lysozyme resistance. Deletion of pbpA1 corrected this effect, demonstrating that PBP A1 is also involved in this. Susceptibility to lysozyme mainly depends on two peptidoglycan modifying enzymes: The peptidoglycan N‐deacetylase PgdA and the peptidoglycan O‐acetyltransferase OatA. Genetic and biochemical experiments consistently demonstrated that the increased lysozyme resistance of the ΔgpsB mutant was PgdA‐dependent and OatA‐independent. Protein‐protein interaction studies supported the idea that GpsB, PBP A1 and PgdA form a complex in L. monocytogenes and identified the regions in PBP A1 and PgdA required for complex formation. These results establish a physiological connection between GpsB, PBP A1 and the peptidoglycan modifying enzyme PgdA. To our knowledge, this is the first reported link between a GpsB‐like cell division protein and factors important for escape from the host immune system.
Arteriovenous Malformation of the Parotid Gland: Case Report and Review of the Literature

In adults, an arteriovenous malformation is a rare presentation of a parotid mass with only a few cases reported in the literature. The clinical picture and behavior may be quite misleading. Careful examination with a high index of suspicion may reveal certain characteristic symptoms, signs and radiologic findings. A rare case of arteriovenous malformation of the parotid gland is presented with a brief review of the diagnostic workup and treatment of such lesions.
Genetic and phenotypic characterization of Candida albicans strains isolated from infectious disease patients in Shanghai.

Candida albicans, as an opportunistic pathogen, can cause superficial and life-threatening candidiasis in immunocompromised individuals. The formation of surface-associated biofilms and the appearance of drug resistance pose a significant challenge for clinical intervention. In this study, a total of 104 hospital-acquired C. alibcans clinical isolates were collected from sterile sites and mucosal lesions of 92 infectious disease patients in the Shanghai Public Health Clinical Center and analysed. The resistance rates to fluconazole, itraconazole and voriconazole were 12.5 %, 15.4 % and 11.5 % respectively. Multilocus sequence typing (MLST) analysis identified 63 diploid sequence types (DSTs) with a decentralized phylogeny, of which 37 DSTs (58.7 %) had not been reported in the online MLST database. Loss of heterozygosity was observed in ACC1 and ADP1 sequences obtained from six sequential isolates from a patient receiving antifungal treatment, which exemplified the effect of microevolution on C. albicans genetic alterations. Biofilm formation capability, an important virulence trait of C. albicans, was variable among strains isolated from different anatomical sites (P = 0.0302) and affected by genotypes (P = 0.0185). The mRNA levels of the azole antifungal target ERG11 gene and efflux pump genes (CDR1, CDR2 and MDR1) were detected in 9-18.1 % of azole-resistant and susceptible-dose dependent (S-DD) isolates. Twelve mutations encoding distinct amino acid substitutions in ERG11 were found in azole-resistant and S-DD isolates. Among them, A114S, Y132H and Y257H substitution in the ERG11 gene may be primarily related to azole resistance. Taken together, we observed a high level of diversity within C. albicans isolates. Multiple inter-related underlying mechanisms, including genetic and environmental factors, may account for high surface adhesion or azole resistance in clinical C. albicans infections.
Decoy NF‐κB fortified immature dendritic cells maintain laryngeal allograft integrity and provide enhancement of regulatory T cells

The increased risk of malignancy associated with post‐transplant immunosuppression limits the potential of laryngeal transplantation as a reconstructive option. This risk may be mitigated by utilizing decoy nuclear factor kappa B (NF‐κB) immature dendritic cells (iDC) to provide donor‐specific tolerance. The purpose of this study was to explore whether tolerogenic properties of iDC can be applied to composite tissue transplantation.
MECHANISMS OF NEURAL REGENERATION. Progress in Brain Research Vol. 13

brain. The way in which this computer may work is illustrated largely by reference to the author's outstanding work upon the octopus. To this is added accounts of the structural characteristics of the human brain, though here the gaps in our knowledge are more apparent than the certainties we have. It is a fascinating book, the reaction to which will be largely determined by temperament. Readers will either be inspired by the vision that we may soon understand the nature of man or depressed by the seemingly infinite gap between hypothesis and fact in our approach to this understanding.
SCIATIC PAIN AND ITS RELIEF BY OPERATIONS ON MUSCLE AND FASCIA

It has long been known that in many cases continued pain referred to the course of the trunk of the sciatic nerve or to the field of distribution of its two main components, the common peroneal and tibial nerves, the pain may be due to extrinsic pressure by a neoplasm or an infiltration either within the pelvis or outside of it; that the pain at times is caused by a new growth within the spinal canal or by organic disease of the radicles beyond the cord proper; that it is sometimes consequent on disease of the lumbar segment of the spine, and that it may be due to inflammatory disease of the nerve itself, as manifested by those clinical signs on which one must rely, as elsewhere, for the recognition of such neuritis. By these signs is meant impairment of the motor power or disturbance of sensation, either superficial or
Bacilliform DNA-containing plant viruses in the tropics: commonalities within a genetically diverse group.

UNLABELLED Plant viruses, possessing a bacilliform shape and containing double-stranded DNA, are emerging as important pathogens in a number of agricultural and horticultural crops in the tropics. They have been reported from a large number of countries in African and Asian continents, as well as from islands from the Pacific region. The viruses, belonging to two genera, Badnavirus and Tungrovirus, within the family Caulimoviridae, have genomes displaying a common plan, yet are highly variable, sometimes even between isolates of the same virus. In this article, we summarize the current knowledge with a view to revealing the common features embedded within the genetic diversity of this group of viruses. TAXONOMY Virus; order Unassigned; family Caulimoviridae; genera Badnavirus and Tungrovirus; species Banana streak viruses, Bougainvillea spectabilis chlorotic vein banding virus, Cacao swollen shoot virus, Citrus yellow mosaic badnavirus, Dioscorea bacilliform viruses, Rice tungro bacilliform virus, Sugarcane bacilliform viruses and Taro bacilliform virus. MICROBIOLOGICAL PROPERTIES Bacilliform in shape; length, 60-900 nm; width, 35-50 nm; circular double-stranded DNA of approximately 7.5 kbp with one or more single-stranded discontinuities. HOST RANGE Each virus generally limited to its own host, including banana, bougainvillea, black pepper, cacao, citrus species, Dioscorea alata, rice, sugarcane and taro. DISEASE SYMPTOMS Foliar streaking in banana and sugarcane, swelling of shoots in cacao, yellow mosaic in leaves and stems in citrus, brown spot in the tubers in yam and yellow-orange discoloration and stunting in rice. USEFUL WEBSITES http://www.dpvweb. net.
Characterization of human papillomavirus type 11‐specific immune responses in a preclinical model

Human papillomavirus (HPV) types 6 and 11 are associated with recurrent respiratory papillomatosis (RRP). Although a prophylactic vaccine has been developed that protects against HPV infection, a therapeutic vaccine is still needed for those patients infected with and/or suffering from persistent disease. Therefore, we developed a novel, therapeutic DNA vaccine targeting HPV‐11 and characterized the in vivo immunologic responses generated against HPV‐11 E6 and E7 after DNA vaccination in a preclinical model.
Linear Impulse Osteotome for Rhinoplasty

The 2500 Impactor linear impulse osteotome (MicroAire® Surgical Instruments, Charlottesville, VA) is a new power instrument for the rhinoplasty surgeon. Air pressure drives the osteotome in linear, oscillating pulses, which allows for easy bone cuts. Dorsal hump reduction and a variety of osteotomies were performed on seven cadavers; results were compared with those from traditional osteotome and mallet. Results show equal accuracy and precision, with the degree of soft tissue injury and bone comminution being minimal by each technique. Dorsal hump reduction with the Impactor was performed in a single maneuver starting at the anterior septal angle, cutting easily through the rigid cartilaginous dorsum. The Impactor was used to perform osteotomies on two patients with nasal deformities and satisfactory reductions were achieved. The major distinction with this instrument is the tremendous ease with which bone cuts are made. Minimal pressure is needed as the Impactor advances through bone. In addition, the Impactor offers single operator use and a unique method of reducing a prominent nasal dorsum.
Host perception of jasmonates promotes infection by Fusarium oxysporum formae speciales that produce isoleucine- and leucine-conjugated jasmonates.

Three pathogenic forms, or formae speciales (f. spp.), of Fusarium oxysporum infect the roots of Arabidopsis thaliana below ground, instigating symptoms of wilt disease in leaves above ground. In previous reports, Arabidopsis mutants that are deficient in the biosynthesis of abscisic acid or salicylic acid or insensitive to ethylene or jasmonates exhibited either more or less wilt disease, than the wild-type, implicating the involvement of hormones in the normal host response to F. oxysporum. Our analysis of hormone-related mutants finds no evidence that endogenous hormones contribute to infection in roots. Mutants that are deficient in abscisic acid and insensitive to ethylene show no less infection than the wild-type, although they exhibit less disease. Whether a mutant that is insensitive to jasmonates affects infection depends on which forma specialis (f. sp.) is infecting the roots. Insensitivity to jasmonates suppresses infection by F. oxysporum f. sp. conglutinans and F. oxysporum f. sp. matthioli, which produce isoleucine- and leucine-conjugated jasmonate (JA-Ile/Leu), respectively, in culture filtrates, whereas insensitivity to jasmonates has no effect on infection by F. oxysporum f. sp. raphani, which produces no detectable JA-Ile/Leu. Furthermore, insensitivity to jasmonates has no effect on wilt disease of tomato, and the tomato pathogen F. oxysporum f. sp. lycopersici produces no detectable jasmonates. Thus, some, but not all, F. oxysporum pathogens appear to utilize jasmonates as effectors, promoting infection in roots and/or the development of symptoms in shoots. Only when the infection of roots is promoted by jasmonates is wilt disease enhanced in a mutant deficient in salicylic acid biosynthesis.
Iris yellow spot virus (Tospovirus: Bunyaviridae): from obscurity to research priority.

TAXONOMY Iris yellow spot virus (IYSV) is in the genus Tospovirus, family Bunyaviridae, with a single-stranded, tri-segmented RNA genome with an ambisense genome organization. Members of the other genera in the family infect predominantly vertebrates and insects. GEOGRAPHICAL DISTRIBUTION IYSV is present in most Allium-growing regions of the world. PHYSICAL PROPERTIES Virions are pleomorphic particles of 80-120 nm in size. The particle consists of RNA, protein, glycoprotein and lipids. GENOME IYSV shares the genomic features of other tospoviruses: a segmented RNA genome of three RNAs, referred to as large (L), medium (M) and small (S). The L RNA codes for the RNA-dependent RNA polymerase (RdRp) in negative sense. The M RNA uses an ambisense coding strategy and codes for the precursor for the GN /GC glycoprotein in the viral complementary (vc) sense and a non-structural protein (NSm) in the viral (v) sense. The S RNA also uses an ambisense coding strategy with the coat protein (N) in vc sense and a non-structural protein (NSs) in the v sense. TRANSMISSION The virus is transmitted by Thrips tabaci Lindeman (Order: Thysanoptera; Family: Thripidae; onion thrips) and with less efficiency by Frankliniella fusca Hinds (tobacco thrips). HOST: IYSV has a relatively broad host range, including cultivated and wild onions, garlic, chives, leeks and several ornamentals. Some weeds are naturally infected by IYSV and may serve as alternative hosts for the virus. SYMPTOMS IYSV symptoms in Allium spp. are yellow- to straw-coloured, diamond-shaped lesions on leaves and flowering scapes. Diamond-shaped lesions are particularly pronounced on scapes. As the disease progresses, the lesions coalesce, leading to lodging of the scapes. In seed crops, this could lead to a reduction in yield and quality. Early to mid-season infection in bulb crops results in reduced vigour and bulb size. CONTROL Resistant varieties are not available, but a limited number of accessions with field tolerance have been identified. Integrated disease management tactics, including sanitation, crop rotation, thrips management, maintenance of optimal plant vigour, soil fertility, irrigation and physical separation of bulb and seed crops, can mitigate the effect of the disease. Virus code: 00.011. 0.85. 009 Useful link: http://www.alliumnet. com/.
Proteinuria reduction and progression to renal failure in patients with type 2 diabetes mellitus and overt nephropathy.

BACKGROUND Little is known of the effects of blood pressure reduction by specific classes of antihypertensive drugs on the association between proteinuria reduction and progression of kidney insufficiency and development of end-stage kidney disease in patients with overt diabetic nephropathy in type 2 diabetes mellitus. METHODS Associations between baseline proteinuria and proteinuria reduction by either irbesartan, amlodipine, or control for similar decrements in blood pressure and the cumulative incidence of renal end points were examined using the Kaplan-Meier method in patients enrolled in the Irbesartan Diabetic Nephropathy Trial. RESULTS Risk for kidney failure doubled for each doubling of baseline proteinuria level (hazard ratio, 2.04; 95% confidence interval, 1.87 to 2.22; P < 0.001). For each halving of proteinuria level between baseline and 12 months with treatment, risk for kidney failure was reduced by more than half (hazard ratio, 0.44; 95% confidence interval, 0.40 to 0.49; P < 0.001). For the same proportional change in proteinuria, the reduction in risk for kidney failure was significantly greater for irbesartan compared with amlodipine ( P = 0.048), but not control ( P = 0.245). Proteinuria reduction in the first 12 months of therapy with irbesartan is associated with 36% of the total renoprotective effect observed. CONCLUSION Baseline proteinuria is an important risk factor for kidney failure and provides a means to identify patients at greatest risk. Halving proteinuria halves the kidney risk. Proteinuria reduction using an angiotensin receptor-blocking agent, such as irbesartan, should be regarded as an important therapeutic goal in renoprotective strategies.
A Case Report of Ectopic Cervical Thymoma : A New Approach for a Preoperative Diagnosis

We report an unusual case of ectopic cervical thymoma. A 35-year-old female patient presented with an anterior neck mass that developed over a five-month duration. The patient underwent fine-needle aspiration cytology (FNAC) twice, but the tumor type could not be diagnosed. The surgically removed tumor was white in color and had a smooth surface. According to the postoperative pathological examination, the tumor was diagnosed as a Stage I ectopic cervical thymoma and Type B1 according to the Masaoka staging system and the World Health Organization (WHO) histological staging system, respectively. The patient was in good overall health and remained without tumor recurrence at the time of the 10-month follow-up. Because it was difficult to make a preoperative definite diagnosis by FNAC for the thymoma, we constructed a cell block from the existing cytological specimen. Immunohistological staining using the cell-block method clearly demonstrated the biphasic cellular population pattern that is a characteristic of thymoma. Therefore, this method may be useful as a preoperative differential diagnostic modality for cervical thymomas.
Critical trust: understanding lay perceptions of health and safety risk regulation

The binary opposition of trusting or not trusting is inadequate to understand the often ambiguous and contradictory ideas people possess about risk regulators, particularly when knowledge and experience of such institutions is limited. The paper reports qualitative and quantitative data from a major study of public perceptions (n = 30 focus groups) of UK risk regulators. We compare the complex and widely different ‘trust profiles’ of two regulatory organisations which are institutionally related (the Health and Safety Executive and the Railways Inspectorate) but very separate in the minds of our participants. The paper develops the notion of critical trust to interrogate the various ways in which people make sense of such organisations, as well as discussing the modes of reasoning that people deploy. The paper argues that views of participants are the outcome of a reconciliation of diverse perceptions concerning the role of the organisation, structural factors and the nature of the regulated risk.
Transmastoid resurfacing of superior semicircular canal dehiscence

To describe a new and fast surgical technique in treating superior semicircular canal dehiscence syndrome by resurfacing the canal defect via the transmastoid approach without retraction of the whole temporal lobe and to demonstrate the clinical and audiologic results of the superior canal dehiscence repair. Superior semicircular canal dehiscence syndrome is a well‐described pathology. Surgical procedures through the middle fossa approach to resurface the superior canal and transmastoid plugging are considered the main surgical therapeutic options for patients with debilitating symptoms. Both have drawbacks; plugging is invasive to the inner ear, and resurfacing requires a middle fossa approach.