Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationships in the genus Hordeum: Giemsa C-banded karyotypes

Giemsa C-banded karyotypes of the 32 Hordeum L. species incl. all subspecies and cytotypes divide them into four groups by chromosome banding patterns. Most taxa have a rather similar pattern with a number of more or less randomly disposed C-bands at centromeric, intercalary, and distal positions. This agrees with their grouping with a common genome, H. H. brevisubulatum s.l. is normally grouped with genome H, but the banding patterns of the five subspecies deviate by having a low number of centromeric and intercalary bands only (patterns vary from having no to very conspicuous C-bands at the telomeres). H. bulbosum has most C-bands at the centromeres, and H. vulgare, most C-bands at centromeric and juxtacentromeric positions. The overall resemblance of the C-banding patterns of H. bulbosum and H. vulgare supports that both carry the same genome, I. H. marinum and H. murinum each have a deviating karyotype. The corresponding genomes are preliminarily referred to as ‘X’ and ‘V’. In combination with chromosome number, and number and morphology of marker chromosomes, the C-banded karyotypes of a number of species are sufficiently distinct to be of use for identification and the study of relationships. Most Hordeum species of the Americas have similar C-banded karyotypes at the respective ploidy level, questioning the biological relevance of referring them to different sections.
Overexpression of formate dehydrogenase inArabidopsis thaliana resulted in plants tolerant to high concentrations of formate

Summary The potential role played by formate dehydrogenase (FDH) in formate metabolism has been examined by the overexpression of FDH in Arabidopsis thaliana . Three independent transgenic lines were selected and shown to produce elevated amounts of FDH protein with a corresponding elevated FDH activity (2.5-5 fold) over wild-type (WT) plants. Under normal growth conditions, no altered phenotype was observed in these transgenic plants; in growth media supplied with formate, however, significant differences in shoot and root growth, compared to that of WT plants, were observed. WT plants were severely injured if grown in the presence of 16 mmol/L formate, while the transgenic plants were able to grow well. Formate delayed germination of both WT and transgenic seeds at concentrations above 4 mmol/L, but both types of seeds were eventually able to complete more than 95 % germination even at 32 mmol/L formate. Formate markedly inhibited primary root elongation, and its inhibitory action on WT was much stronger than on transgenic plants. Different formate salts affected root elongation similarly, indicating that the formate ion was the major factor inhibiting root growth. Sodium acetate (NaAc), an analogue of formate, also inhibited root elongation, but its action on WT and transgenic plants was the same, indicating that tolerance of transgenic plants to formate toxicity was specific. Transgenic plants showed no significant tolerance to the toxicity of two other one-carbon metabolites, methanol and formaldehyde. A role for FDH in detoxifying formate is proposed.
Adaptation of the C4 grass Panicum maximum to defoliation is related to plasticity of N uptake, mobilisation and allocation patterns

Dry mass production and persistence of Panicum maximum pastures depends on nitrogen supply. Defoliation influences N uptake and allocation patterns yet its effects on plasticity of N dynamics in P. maximum have not been investigated. Stable isotopes of N (15N) were used in order to test the hypothesis that defoliation in terms of proportion of the leaf area removed effects N mobilisation, uptake and allocation patterns in P. maximum. The plants were initially cut weekly to a height of either 0.15 m or 0.30 m for seven weeks. Eight weeks after the first defoliation, all plants were defoliated for a final time to remove 0, 25, 50, 75 or 100 % of the area of each individual leaf blade of the main tiller. Root N uptake was reduced when all leaf area was removed, but more lenient defoliation improved N uptake due to a positive effect on specific N uptake. Young leaves, side tillers and roots were the main sinks for N from root uptake. Roots of P. maximum became a net source of N for mobilisation immediately after severe defoliation. Root uptake was the main source of N for new growth in P. maximum plants. Allocation pattern of mobilised N was different from that of N derived from root uptake. It was concluded that adaptation of P. maximum to defoliation is related to plasticity of N uptake, mobilisation and allocation, but changes in N dynamics did not offset negative impacts of complete defoliation of the plants.
Numerical investigation of the optimal control rule for decision‐making in fisheries management

: Recently, control rules (CR) have been widely used for decision-making of fisheries management. A CR describes fishing pressure (usually fishing mortality, F) as a function of some other variable(s) related to the status of the stock. The prevailing CR aim to achieve FMSY. The main idea of CR is to change fishing pressure based on stock conditions. Therefore, it seems irrational that the goals of prevailing CR are defined by the constant harvesting rate (CHR) strategy. The objective of the present study was to develop a method by which to numerically search for the optimal CR, apart from the traditional biological reference points based on CHR. I also compared the performance of the optimal CR and those of the prevailing CR (FMSY, 75%FMSY, New Management Procedure of the International Whaling Committee and the CR in US guidelines). The result suggested that the limitation of maximum fishing mortality was effective for stocks with low natural mortality and large stock size estimation error, while the biomass threshold was effective for stocks with short longevity and small estimation error. This means that the optimal CR is sensitive to the life history and uncertainty of the stock. Therefore, there seems to be no ‘one-size-fits-all’ rule for fish stocks.
Bariatric surgery in severely obese adolescents – a single centre experience

Background Increasing numbers of severely obese young people undergo bariatric surgery in the USA with reports of 58-73 % of excess weight lost after one year. In 2006, NICE suggested considering surgery for young people in ‘exceptional circumstances’. We present 5 patients operated upon between 2005-2011 at our centre focussing on the ethical and clinical dilemmas faced when establishing a service. Case series/methods Five patients (4 male) aged 14-16 years (mean age 15.25) underwent bariatric surgery. Initial cases were discussed by the local clinical ethics committee prior to the procedures. Mean pre-operative BMI was 60.3 kg/m2 and BMI SDS + 4.3. Co-morbidities included hypertension, insulin resistance, obstructive sleep apnoea, limited mobility and psychosocial issues. All 5 patients had prior involvement with local weight management services with no success. Three of the patients had tried drug treatment with orlistat and/or sibutramine (before it was withdrawn). Two patients were referred from outside the region. Three laparoscopic gastric bypass procedures, 1 laparoscopic gastric banding (patient had a gastric balloon prior to band) and 1 laparoscopic sleeve gastrectomy was performed. No major post operative procedural complications were noted (one patient had a port-rotation) and patients were discharged home within 48 hours. Results Mean percentage of weight loss as a percentage of total body weight at 3 months and 6 months was 11% and 13.25% respectively. Three year data for 1 patient showed 15% weight loss but disappointingly at 5 years, this has not been sustained. Mean BMI at 3 months post procedure was 53 kg/m2 and BMI SDS +4.1. Mean BMI and BMI SDS at 6 months was 51 and +4.0. Resolution of hypertension, increased physical activity and improved school attendance were some of the benefits noted. None of the patients have developed T2DM. Conclusion Recent systematic reviews and meta-analyses suggest that bariatric surgery results in sustained and clinically significant reduction in BMI in adolescents. There were no significant changes recommended in the 2011 review of the previous NICE guidance. Short term follow up data on our cohort of patients' shows initial significant weight loss but less than would be suggested from previous data. Longer term outcomes need to be followed. The surgical option should continue to be exercised with extreme caution at specialist units and only in severely obese adolescents.
Reply:

We thank Drs Sarikaya and McKinney for their response to our article entitled “The Relation of Carotid Calcium Volume with Carotid Artery Stenosis in Symptomatic Patients” and would hereby like to respond to some of their very meaningful discussion points. We certainly agree that there is a large difference in the definition of the domain between our study and the 2 studies performed by their group. In our study, we have correlated the calcium volume with the degree of stenosis of the carotid artery in a population of high-risk patients with recent neurologic symptoms. In the studies of Sarikaya et al and McKinney et al, the relation between carotid artery stenosis and calcium volume was investigated in a more “general” patient population. The difference in patient population follows from the different objectives. Sarikaya et al and McKinney et al investigated the role of calcium volume in screening patients at risk, whereas our study explored the possibility of using calcium volume to identify stenoses of 70%. In current clinical practice, the degree of stenosis of the internal carotid artery is used in the decision to perform carotid endarterectomy, because it is the strongest predictor of its effect. With such a difference in objectives and in patient domain, it is actually not surprising to observe a spectrum effect. However, the extent of this effect was beyond our expectations. The second issue that was addressed by Sarikaya and McKinney is that in our article, we presented the diagnostic accuracy for thresholds different from the optimal value reported in their articles, 0.06 cm. We actually used a whole range of thresholds, including 0.06 cm, as presented in the receiver operating characteristic analysis curve (Fig 3 in our article). This curve shows that for all thresholds, the diagnostic accuracy is rather poor. We presented the diagnostic accuracy for 0.03 and 0.09 cm to illustrate the outer ends of the range of sensitivity and specificity of the calcium volume based stenosis detection for our patient population. However, a direct comparison would benefit from the presentation of the values for the 0.06-cm threshold. We acknowledge Sarikaya and McKinney for observing the weak correlation of calcium volume and the degree of stenosis of the carotid artery on the unaffected side, as opposed to the absence of such a correlation on the affected side. This suggests a stronger correlation of calcium volume and degree of stenosis in asymptomatic patients or arteries. We also thought this was a puzzling finding. Hypothetically, it may express a relation of plaque composition and potential neurologic symptoms. Actually, we have performed a study in the same patient population in which we correlated the intracranial calcium volume burden with intracranial stenosis, which we hope to publish soon. In this study, we actually confirmed the correlation of calcium volume and stenosis in the intracranial arteries. We agree with Sarikaya and McKinney that the role of carotid artery calcium volume and its relation with various neurologic symptoms requires additional research effort.
Infectivity, survival and pathology of Finnish strains of Phytophthora plurivora and Ph. pini in Norway spruce

Abstract The recently described Phytophthora plurivora T. Jung & T.I. Burgess and its close relative Phytophthora pini L.H. Leonian are new arrivals in Finnish horticulture. The objective of this study was to determine whether these species pose a threat to the seedling production of Norway spruce (Picea abies L.), one of the most important tree species in Fennoscandia. Seedlings of P. abies were inoculated on a needle scar with mycelium or on healthy tissue with a suspension of zoospores. All of the Ph. plurivora and Ph. pini isolates produced 100% incidence of disease when needle scars were inoculated with mycelium. Results show that nonwounded shoots of P. abies are also susceptible to infection via zoospores. In this case, 32% of seedlings became symptomatic and signs of wilting developed 4 days post-inoculation (dpi). Histology revealed that zoospore infections of Ph. plurivora led to colonization of almost all shoot tissues including the vascular system and pith parenchyma in less than 4 days. Necrotrophic growth was observed but no latent infection was found. Finnish isolates of Ph. plurivora and Ph. pini had higher growth temperature optima than the other Phytophthora species found in Finland, i.e. Ph. ramorum De Cock & Man in't Veld and Ph. cactorum Lebert & Cohn. All species survived 14 days at −5 °C.
Physiological Aspects of Desiccation Tolerance-A Retrospect

My work on desiccation tolerance was initially inspired by an article published by T. C. Hsiao (1970), in which he showed that when seedlings of maize were subjected to relatively mild stresses, their polysomal complement, and hence their capacity for protein synthesis, declined markedly. On returning the seedlings to a fully hydrated state, polysomes increased to hydrated control levels within an hour, or more, depending upon the severity of the prior stress. Maize seedlings, of course, can withstand only relatively mild stress, but the question that sprang to mind was, What is the fate of the protein-synthesizing complex in a plant, or plant part, that can withstand extremes of drought stress, namely, desiccation? Many plants, particularly lower plants, can lose water to an extent that their moisture content is in equilibrium with the surrounding air. There are many examples of algae, mosses, and lichens that are desiccation tolerant, and several ferns and angiosperms, although, of course, many of the seeds of the latter exhibit "orthodox" qualities, in that they are shed and retain viability in the dry state (Gaff 1977; Gaff and Latz 1978; Bewley 1979; Bewley and Krochko 1982).
Medical Therapy for Endometriosis: Endocrine Pharmacology

Reproductive endocrinologists are challenged daily by the complex problems of patients with infertility and/or pelvic pain who have documented endometriosis. The clinical management of these patients stimulates a host of questions which are yet to be definitively answered: What is the relationship between endometriosis and infertility? Should mild endometriosis be treated? In what clinical settings do medical, surgical or combination therapy represent the optimal management strategy? What is the best medical therapy? How can iatrogenic damage be avoided when surgery is required? After therapy, what is the recurrence rate? What is the best strategy for the prevention of endometriosis and prevention of its progression? Owing to complexities and expense of designing critical clinical studies of endometriosis, it is possible that many of these questions will never be unequivocally answered. Rapid advances are currently being made, however, in the development of hormonal agents for the treatment of endometriosis. These advances have been catalyzed by the current revolution in molecular and cell biology. Reproductive mechanisms are being explored at the molecular level with an emphasis on hormone-receptor, and receptor-DNA interactions. These investigations have provided a rational basis for designing specific pharmacologic agents for the treatment of endometriosis. This review will be divided into two parts: (1) a discussion of the molecular pathogenesis of endometriosis and (2) an evaluation of the endocrine pharmacology of the agents available for the treatment of endometriosis.
Biochemical Modifications and Enhancement of Psoralen Content in Salt-Stressed Seedlings of Psoralea corylifolia Linn.

Salt stress is one of the major global problem rendering vast area of land unsuitable for cultivation. Attempts are therefore directed to screen for salt-tolerant plants for the reclamation of the waste-land. The present study was an attempt to search for the salt tolerance potential of an important endangered medicinal plant Psoralea corylifolia, which is the commercial source of psoralen. Psoralea seeds grown on different concentrations of NaCl exhibited variation in percent germination; however, 25 mM NaCl proved better than control and exhibited maximum percent germination with high shoot and root length. Chlorophyll a, b and a+b decreased on higher concentrations of NaCl. Protein content decreased from 50–100 mM NaCl and then again there was an increase from 110 mM NaCl. Psoralen content exhibited variation in salt-stressed seedlings and maximum psoralen was observed in 25 mM NaCl concentration.
Effects of different dietary lipids on growth and tissue fatty acid changes in fry of the carp Catla catla (Hamilton)

A study was conducted with fry of Catla catla (Hamilton) to investigate the effects of dietary lipid supplements on growth, feed conversion, tissue fatty acid composition and the intestinal lipase activity. Four treatment diets were prepared using purified ingredients incorporating sunflower oil (n-6 fatty acids), cod liver oil (n-3 fatty acid source) and a mixture (1:1) of sunflower and cod liver oil in three diets. The fourth diet was lipid-free and served as the control. The best growth and survival was recorded for fish given the diet having a mixture of n-3 and n-6 fatty acids (weight gain was 380% and survival was 93%), followed by the n-6 diet (320% and 88%), the n-3 diet (290% and 84%) and the lipid-free diet (239.9% and 82%). Feed conversion ratio (FCR) and per cent protein deposited (PPD) followed a similar trend. The intestinal lipase activity (expressed as μg α-naphthol liberated mg_1 protein hr-1) was 83.3, 74.2, 80.1 and 53.7 for n-3 and n-6, n-6, n-3 and lipid-free diet treatments respectively. The fatty acid profile of the whole body was shown to be influenced by dietary fatty acid composition. The results of this laboratory study indicated that a combination of n-3 and n-6 fatty acids is important for growth and survival of this species. The extent to which such observations will be relevant in field conditions can be stated only after results of feeding trials in ponds are available.
Associations between Anurans and Ants in a West African Savanna (Anura: Microhylidae, Hyperoliidae, and Hymenoptera: Formicidae) 1

We report observations and experiments on associations of the frogs, Phrynomantis microps and Kassina fiisca, and the ponerine ants, Megaponera foetens and Paltothyreus tarsatus, in a West African savanna. Several experiments show that the tolerant behavior of the ants toward these frogs is due to chemical components of the frogs' skin. Comparisons to other syntopic frog species suggest that this enables these frogs to make use of burrows that otherwise are unavailable. This is advantageous because in the savanna, most hiding places that remain moist during the dry season are occupied by ants.
Alternative use of food resources causes intra-cohort variation in the size distribution of young-of-the-year perch (Perca fluviatilis)

– Body sizes of young-of-the-year (YOY) perch (Perca fluviatilis) at the end of their first summer are extremely variable and range in different studies between 4 and 15 cm. To analyse whether size divergences in YOY perch may be attributed to alternative use of food resources, adult perch were stocked into two previously fishless ponds and growth, size distribution and food intake of the YOY perch were recorded. In addition to perch, adult bream (Abramis brama) were introduced to produce juvenile bream that could serve as a food resource for YOY perch. The body sizes of YOY perch at the end of the experiment ranged from 32 to 168 mm with a bimodal size distribution. The combination of stomach content analyses and stable isotope signatures revealed that the small size cohort were planctivorous/benthivorous while the large size cohort was piscivorous/cannibalistic. Results implicated that different feeding behaviour contributed to the size divergences in YOY perch and that the extreme growth of the large size cohort was induced by piscivory.
Mesothelin

Mesothelin is a differentiation antigen present on normal mesothelial cells and overexpressed in several human tumors, including mesothelioma and ovarian and pancreatic adenocarcinoma. The mesothelin gene encodes a precursor protein that is processed to yield the 40-kDa protein, mesothelin, attached to the cell membrane by a glycosylphosphatidyl inositol linkage and a 31-kDa shed fragment named megakaryocyte-potentiating factor. The biological function of mesothelin is not known. Mesothelin is a promising candidate for tumor-specific therapy, given its limited expression in normal tissues and high expression in several cancers. SS1(dsFv)PE38 is a recombinant anti-mesothelin immunotoxin that is undergoing clinical evaluation in patients with mesothelin-expressing tumors. There is evidence that mesothelin is an immunogenic protein and could be exploited as a therapeutic cancer vaccine. A soluble mesothelin variant has been identified and could be a useful tumor marker for malignant mesotheliomas.
Numerous chloroplast DNA polymorphisms are shared among different populations and species in the aureoid Senecio (Packera) complex

Species boundaries within the aureoid Senecio complex (Packera) are poorly defined, possibly as a result of hybridization and introgression. The results of restriction site analysis of cpDNA using 16 enzymes and hybridization with lettuce probes representing over 95% of the chloroplast genome reveal a high level of intrapopulational polymorphism combined with a relatively low level of interspecific variation. Forty-nine populations representing 23 different species were examined, and only 20 variable restriction sites were identified. Eleven of the 20 variable sites were polymorphic in at least one population, and 14 of the 23 species were polymorphic for at least one site. The polymorphisms are widespread and are found in species representing all of the previously recognized subgroups of the aureoid complex. Individuals analyzed separately were shown to possess only a single haplorype. Although the polymorphisms may be the result of hybridization and introgression, it is difficult to explain the geograph.
The anatomy of the male genital ducts in the fowl

The epididymis in the male bird consists of the rete testis, ductuli efferentia, and epididymal tubules. The rete testis is lined with cuboidal epithelium not resting on a basement membrane. When distended with sperm the epithelium appears squamous‐like. The tubuli efferentia are lined for the most part with pseudostratied ciliated columnar epithelium resting on a basement membrane. The epithelium is thrown into permanent longitudinal ridges. The epididymal tubules are lined with ciliated columnar epithelium resting on a bastment membrane.