New vineyard cultivation practices create patchy ground vegetation, favouring Woodlarks

Intensive agriculture, in which detrimental farming practices lessen food abundance and/or reduce food accessibility for many animal species, has led to a widespread collapse of farmland biodiversity. Vineyards in central and southern Europe are intensively cultivated; though they may still harbour several rare plant and animal species, they remain little studied. Over the past decades, there has been a considerable reduction in the application of insecticides in wine production, with a progressive shift to biological control (integrated production) and, to a lesser extent, organic production. Spraying of herbicides has also diminished, which has led to more vegetation cover on the ground, although most vineyards remain bare, especially in southern Europe. The effects of these potentially positive environmental trends upon biodiversity remain mostly unknown as regards vertebrates. The Woodlark (Lullula arborea) is an endangered, short-distance migratory bird that forages and breeds on the ground. In southern Switzerland (Valais), it occurs mostly in vineyards. We used radiotracking and mixed effects logistic regression models to assess Woodlark response to modern vineyard farming practices, study factors driving foraging micro-habitat selection, and determine optimal habitat profile to inform management. The presence of ground vegetation cover was the main factor dictating the selection of foraging locations, with an optimum around 55% at the foraging patch scale. These conditions are met in integrated production vineyards, but only when grass is tolerated on part of the ground surface, which is the case on ca. 5% of the total Valais vineyard area. In contrast, conventionally managed vineyards covering a parts per thousand yen95% of the vineyard area are too bare because of systematic application of herbicides all over the ground, whilst the rare organic vineyards usually have a too-dense sward. The optimal mosaic with ca. 50% ground vegetation cover is currently achieved in integrated production vineyards where herbicide is applied every second row. In organic production, ca. 50% ground vegetation cover should be promoted, which requires regular mechanical removal of ground vegetation. These measures are likely to benefit general biodiversity in vineyards.

Pattern recognition ecological niche models fit to presence-only and presence-absence data

1. Identifying the boundary of a species' niche from observational and environmental data is a common problem in ecology and conservation biology and a variety of techniques have been developed or applied to model niches and predict distributions. Here, we examine the performance of some pattern-recognition methods as ecological niche models (ENMs). Particularly, one-class pattern recognition is a flexible and seldom used methodology for modelling ecological niches and distributions from presence-only data. The development of one-class methods that perform comparably to two-class methods (for presence/absence data) would remove modelling decisions about sampling pseudo-absences or background data points when absence points are unavailable. 2. We studied nine methods for one-class classification and seven methods for two-class classification (five common to both), all primarily used in pattern recognition and therefore not common in species distribution and ecological niche modelling, across a set of 106 mountain plant species for which presence-absence data was available. We assessed accuracy using standard metrics and compared trade-offs in omission and commission errors between classification groups as well as effects of prevalence and spatial autocorrelation on accuracy. 3. One-class models fit to presence-only data were comparable to two-class models fit to presence-absence data when performance was evaluated with a measure weighting omission and commission errors equally. One-class models were superior for reducing omission errors (i.e. yielding higher sensitivity), and two-classes models were superior for reducing commission errors (i.e. yielding higher specificity). For these methods, spatial autocorrelation was only influential when prevalence was low. 4. These results differ from previous efforts to evaluate alternative modelling approaches to build ENM and are particularly noteworthy because data are from exhaustively sampled populations minimizing false absence records. Accurate, transferable models of species' ecological niches and distributions are needed to advance ecological research and are crucial for effective environmental planning and conservation; the pattern-recognition approaches studied here show good potential for future modelling studies. This study also provides an introduction to promising methods for ecological modelling inherited from the pattern-recognition discipline.

Pattern and clinical significance of cancer-testis gene expression in head and neck squamous cell carcinoma

Les cancer-testis antigènes appartiennent à la famille des antigènes tumoraux spécifiques. Ils ont montré un pouvoir immunogène chez les patients porteurs de différents cancers. En effet, ils stimulent sélectivement les lymphocytes cytotoxiques, et leur expression spécifique dans les tissus tumoraux en fait une cible idéale pour une vaccination antitumorale. Le but de cette étude est d'identifier l'expression de certains de ces antigènes, d'analyser leur valeur pronostique et de déterminer la meilleure cible antigénique pour permettre une immunothérapie spécifique dans les carcinomes épidermoïdes des voies aérodigestives supérieures. Le profil et le taux d'expression de 12 cancer-testis antigènes (MAGE-A1, MAGE-A3, MAGE-A4, MAGEA10, MAGE-C2, NY-ESO-1, LAGE-1, SSX-2, SSX-4, BAGE, GAGE-1/2, GAGE-3/4) et de 3 autres antigènes tumoraux spécifiques (PRAME, HERV-K-MEL, NA-17A) ont été évalués par RT-PCR sur 57 échantillons de cancers ORL primaires. Les paramètres tumoraux et cliniques ont été prospectivement collectés afin de corréler ces données avec le résultat de nos investigations immunobiologiques. Quatre-vingt-huit pour cent des tumeurs expriment au moins 1 antigène. Une co-expression de 3 gènes ou plus est détectée chez 59% des patients. MAGE-A4 (60%), MAGE-A3 (51%), PRAME (49%) et HERV-K-MEL (42%) sont les gènes le plus fréquemment exprimés. Ils sont totalement absents des muqueuses saines avoisinantes. La présence de MAGE-A et NY-ESO-1 à la surface des cellules a été vérifiée par immunohistochimie. Nos analyses statistiques ont permis d'identifier une diminution de la survie liée au cancer chez les patients porteurs d'une tumeur exprimant de multiples cancer-testis antigènes et notamment MAGE-A4 dont l'expression indépendante d'autres éléments cliniques s'associe statistiquement à un taux de survie diminué. Nos résultats ont permis d'identifier un rôle pronostique de l'expression des gènes associés aux tumeurs dont l'expression est apparemment liée à un phénotype de malignité plus élevé. Cette constatation, corroborée par l'identification parallèle d'un infiltrat lymphocytaire spécifique confirme l'utilité potentielle de certains cancer-testis antigènes comme cible pour une immunothérapie ciblée dans les carcinomes des voies aérodigestives supérieures

A clinical pattern-based etiological diagnostic strategy for sensory neuronopathies: a French collaborative study.

Sensory neuronopathies (SNNs) encompass paraneoplastic, infectious, dysimmune, toxic, inherited, and idiopathic disorders. Recently described diagnostic criteria allow SNN to be differentiated from other forms of sensory neuropathy, but there is no validated strategy based on routine clinical investigations for the etiological diagnosis of SNN. In a multicenter study, the clinical, biological, and electrophysiological characteristics of 148 patients with SNN were analyzed. Multiple correspondence analysis and logistic regression were used to identify patterns differentiating between forms of SNNs with different etiologies. Models were constructed using a study population of 88 patients and checked using a test population of 60 cases. Four patterns were identified. Pattern A, with an acute or subacute onset in the four limbs or arms, early pain, and frequently affecting males over 60 years of age, identified mainly paraneoplastic, toxic, and infectious SNN. Pattern B identified patients with progressive SNN and was divided into patterns C and D, the former corresponding to patients with inherited or slowly progressive idiopathic SNN with severe ataxia and electrophysiological abnormalities and the latter to patients with idiopathic, dysimmune, and sometimes paraneoplastic SNN with a more rapid course than in pattern C. The diagnostic strategy based on these patterns correctly identified 84/88 and 58/60 patients in the study and test populations, respectively.

Early co-occurrence of a neurologic-psychiatric disease pattern in Niemann-Pick type C disease: a retrospective Swiss cohort study.

BackgroundNiemann-Pick disease type C (NP-C) is a rare autosomal recessive disorder of lysosomal cholesterol transport. The objective of this retrospective cohort study was to critically analyze the onset and time course of symptoms, and the clinical diagnostic work-up in the Swiss NP-C cohort.MethodsClinical, biochemical and genetic data were assessed for 14 patients derived from 9 families diagnosed with NP-C between 1994 and 2013. We retrospectively evaluated diagnostic delays and period prevalence rates for neurological, psychiatric and visceral symptoms associated with NP-C disease. The NP-C suspicion index was calculated for the time of neurological disease onset and the time of diagnosis.ResultsThe shortest median diagnostic delay was noted for vertical supranuclear gaze palsy (2y). Ataxia, dysarthria, dysphagia, spasticity, cataplexy, seizures and cognitive decline displayed similar median diagnostic delays (4¿5y). The longest median diagnostic delay was associated with hepatosplenomegaly (15y). Highest period prevalence rates were noted for ataxia, dysarthria, vertical supranuclear gaze palsy and cognitive decline. The NP-C suspicion index revealed a median score of 81 points in nine patients at the time of neurological disease onset which is highly suspicious for NP-C disease. At the time of diagnosis, the score increased to 206 points.ConclusionA neurologic-psychiatric disease pattern represents the most characteristic clinical manifestation of NP-C and occurs early in the disease course. Visceral manifestation such as isolated hepatosplenomegaly often fails recognition and thus highlights the importance of a work-up for lysosomal storage disorders. The NP-C suspicion index emphasizes the importance of a multisystem evaluation, but seems to be weak in monosymptomatic and infantile NP-C patients.

Evidence for catabolic pathway of propionate metabolism in CNS: expression pattern of methylmalonyl-CoA mutase and propionyl-CoA carboxylase alpha-subunit in developing and adult rat brain.

Methylmalonyl-CoA mutase (MCM) and propionyl-CoA carboxylase (PCC) are the key enzymes of the catabolic pathway of propionate metabolism and are mainly expressed in liver, kidney and heart. Deficiency of these enzymes leads to two classical organic acidurias: methylmalonic and propionic aciduria. Patients with these diseases suffer from a whole spectrum of neurological manifestations that are limiting their quality of life. Current treatment does not seem to effectively prevent neurological deterioration and pathophysiological mechanisms are poorly understood. In this article we show evidence for the expression of the catabolic pathway of propionate metabolism in the developing and adult rat CNS. Both, MCM and PCC enzymes are co-expressed in neurons and found in all regions of the CNS. Disease-specific metabolites such as methylmalonate, propionyl-CoA and 2-methylcitrate could thus be formed autonomously in the CNS and contribute to the pathophysiological mechanisms of neurotoxicity. In rat embryos (E15.5 and E18.5), MCM and PCC show a much higher expression level in the entire CNS than in the liver, suggesting a different, but important function of this pathway during brain development.

Serum glycodelin pattern during the menstrual cycle in healthy young women.

OBJECTIVE: Glycodelin (PP14) is produced by the epithelium of the endometrium and its determination in the serum is used for functional evaluation of this tissue. Given the complex regulation and the combined contraceptive and immunosuppressive roles of glycodelin, the current lack of normal values for its serum concentration in the physiological menstrual cycle, derived from a large sample number, is a problem. We have therefore established reference values from over 600 sera. DESIGN: Retrospective study using banked serum samples. SETTING: University hospital. METHODS: Measurement of blood samples daily or every second day during one full cycle. MAIN OUTCOME MEASURES: Serum concentrations of glycodelin and normal values for every such one- or two-day interval were calculated. Late luteal phase glycodelin levels were compared with ovarian hormones. Follicular phase levels were compared with stimulated cycles from patients undergoing in vitro fertilization. RESULTS: Glycodelin concentrations were low around ovulation. Highest levels were observed at the end of the luteal phase; the glycodelin serum peak was reached 6-8 days after the one for progesterone. Late luteal glycodelin levels correlated negatively with the body mass index and positively with the progesterone level earlier in the secretory (mid-luteal) phase in the same woman. No associations with other ovarian hormones were observed. Follicular phase glycodelin levels were higher in the spontaneous than in the in vitro fertilization cycles. CONCLUSIONS: Normal values taken at two- or one-day intervals demonstrate the very late appearance of high serum glycodelin levels during the physiological menstrual cycle and their correlation with progesterone occurring earlier in the cycle.

Male-pattern baldness susceptibility locus at 20p11.

We conducted a genome-wide association study for androgenic alopecia in 1,125 men and identified a newly associated locus at chromosome 20p11.22, confirmed in three independent cohorts (n = 1,650; OR = 1.60, P = 1.1 x 10(-14) for rs1160312). The one man in seven who harbors risk alleles at both 20p11.22 and AR (encoding the androgen receptor) has a sevenfold-increased odds of androgenic alopecia (OR = 7.12, P = 3.7 x 10(-15)).

Permanent.Plot.ch - a database for Swiss permanent vegetation plots

The aim of the Permanent.Plot.ch project is the conservation of historical data about permanent plots in Switzerland and the monitoring of vegetation in a context of environmental changes (mainly climate and land use). Permanent plots are currently being recognized as valuable tools to monitor long-term effects of environmental changes on vegetation. Often used in short studies (3 to 5 years), they are generally abandoned at the end of projects. However, their full potential might only be revealed after 10 or more years, once the location is lost. For instance, some of the oldest permanent plots in Switzerland (first half of the 20th century) were nearly lost, although they are now very valuable data. The Permanent.Plot.ch national database (GIVD ID EU-CH-001), by storing historical and recent data, will allow to ensuring future access to data from permanent vegetation plots. As the database contains some private data, it is not directly available on internet but an overview of the data can be downloaded from internet (http://www.unil.ch/ppch) and precise data are available on request.

Alterations in the local myocardial motion pattern in patients suffering from pressure overload due to aortic stenosis.

BACKGROUND: MR tissue tagging allows the noninvasive assessment of the locally and temporally resolved motion pattern of the left ventricle. Alterations in cardiac torsion and diastolic relaxation of the left ventricle were studied in patients with aortic stenosis and were compared with those of healthy control subjects and championship rowers with physiological volume-overload hypertrophy. METHODS AND RESULTS: Twelve aortic stenosis patients, 11 healthy control subjects with normal left ventricular function, and 11 world-championship rowers were investigated for systolic and diastolic heart wall motion on a basal and an apical level of the myocardium. Systolic torsion and untwisting during diastole were examined by use of a novel tagging technique (CSPAMM) that provides access to systolic and diastolic motion data. In the healthy heart, the left ventricle performs a systolic wringing motion, with a counterclockwise rotation at the apex and a clockwise rotation at the base. Apical untwisting precedes diastolic filling. In the athlete's heart, torsion and untwisting remain unchanged compared with those of the control subjects. In aortic stenosis patients, torsion is significantly increased and diastolic apical untwisting is prolonged compared with those of control subjects or athletes. CONCLUSIONS: Torsional behavior as observed in pressure- and volume-overloaded hearts is consistent with current theoretical findings. A delayed diastolic untwisting in the pressure-overloaded hearts of the patients may contribute to a tendency toward diastolic dysfunction.

Quality of life depends on the drinking pattern in alcohol-dependent patients.

AIMS: In patients with alcohol dependence, health-related quality of life (QOL) is reduced compared with that of a normal healthy population. The objective of the current analysis was to describe the evolution of health-related QOL in adults with alcohol dependence during a 24-month period after initial assessment for alcohol-related treatment in a routine practice setting, and its relation to drinking pattern which was evaluated across clusters based on the predominant pattern of alcohol use, set against the influence of baseline variables METHODS: The Medical Outcomes Study 36-Item Short-Form Survey (MOS-SF-36) was used to measure QOL at baseline and quarterly for 2 years among participants in CONTROL, a prospective observational study of patients initiating treatment for alcohol dependence. The sample consisted of 160 adults with alcohol dependence (65.6% males) with a mean (SD) age of 45.6 (12.0) years. Alcohol use data were collected using TimeLine Follow-Back. Based on the participant's reported alcohol use, three clusters were identified: 52 (32.5%) mostly abstainers, 64 (40.0%) mostly moderate drinkers and 44 (27.5%) mostly heavy drinkers. Mixed-effect linear regression analysis was used to identify factors that were potentially associated with the mental and physical summary MOS-SF-36 scores at each time point. RESULTS: The mean (SD) MOS-SF-36 mental component summary score (range 0-100, norm 50) was 35.7 (13.6) at baseline [mostly abstainers: 40.4 (14.6); mostly moderate drinkers 35.6 (12.4); mostly heavy drinkers 30.1 (12.1)]. The score improved to 43.1 (13.4) at 3 months [mostly abstainers: 47.4 (12.3); mostly moderate drinkers 44.2 (12.7); mostly heavy drinkers 35.1 (12.9)], to 47.3 (11.4) at 12 months [mostly abstainers: 51.7 (9.7); mostly moderate drinkers 44.8 (11.9); mostly heavy drinkers 44.1 (11.3)], and to 46.6 (11.1) at 24 months [mostly abstainers: 49.2 (11.6); mostly moderate drinkers 45.7 (11.9); mostly heavy drinkers 43.7 (8.8)]. Mixed-effect linear regression multivariate analyses indicated that there was a significant association between a lower 2-year follow-up MOS-SF-36 mental score and being a mostly heavy drinker (-6.97, P < 0.001) or mostly moderate drinker (-3.34 points, P = 0.018) [compared to mostly abstainers], being female (-3.73, P = 0.004), and having a Beck Inventory scale score ≥8 (-6.54, P < 0.001), at baseline. The mean (SD) MOS-SF-36 physical component summary score was 48.8 (10.6) at baseline, remained stable over the follow-up and did not differ across the three clusters. Mixed-effect linear regression univariate analyses found that the average 2-year follow-up MOS-SF-36 physical score was increased (compared with mostly abstainers) in mostly heavy drinkers (+4.44, P = 0.007); no other variables tested influenced the MOS-SF-36 physical score. CONCLUSION: Among individuals with alcohol dependence, a rapid improvement was seen in the mental dimension of QOL following treatment initiation, which was maintained during 24 months. Improvement was associated with the pattern of alcohol use, becoming close to the general population norm in patients classified as mostly abstainers, improving substantially in mostly moderate drinkers and improving only slightly in mostly heavy drinkers. The physical dimension of QOL was generally in the normal range but was not associated with drinking patterns.

Influence of bedrock structures on the spatial pattern of erosional landforms in small alpine catchments

Structural settings and lithological characteristics are traditionally assumed to influence the development of erosional landforms, such as gully networks and rock couloirs, in steep mountain rock basins. The structural control of erosion of two small alpine catchments of distinctive rock types is evaluated by comparing the correspondences between the orientations of their gullies and rock couloirs with (1) the sliding orientations of potential slope failures mechanisms, and (2) the orientation of the maximum joint frequency, this latter being considered as the direction exploited primarily by erosion and mass wasting processes. These characteristic orientations can be interpreted as structural weaknesses contributing to the initiation and propagation of erosion. The morphostructural analysis was performed using digital elevation models and field observations. The catchment comprised of magmatic intrusive rocks shows a clear structural control, mostly expressed through potential wedges failure. Such joint configurations have a particular geometry that encourages the development of gullies in hard rock, e.g. through enhanced gravitational and hydrological erosional processes. In the catchment underlain by sedimentary rocks, penetrative joints that act as structural weaknesses seem to be exploited by gullies and rock couloirs. However, the lithological setting and bedding configuration prominently control the development of erosional landforms, and influence not only the local pattern of geomorphic features, but the general morphology of the catchment. The orientations of the maximum joint frequency are clearly associated with the gully network, suggesting that its development is governed by anisotropy in rock strength. These two catchments are typical of bedrock-dominated basins prone to intense processes of debris supply. This study suggests a quantitative approach for describing the relationship between bedrock jointing and geomorphic features geometry. Incorporation of bedrock structure can be relevant when studying processes governing the transfer of clastic material, for the assessment of sediment yields and in landforms evolution models.

The influence of drinking pattern, at individual and aggregate levels, on alcohol-related negative consequences.

AIM: To determine the extent drinking patterns (at the individual and country level) are associated with alcohol-related consequences over and above the total alcohol the person consumes. METHODS: Hierarchical linear models were estimated based on general population surveys conducted in 18 countries participating in the GENACIS project. RESULTS: In general, the positive association between drinking pattern scores and alcohol-related consequences was found at both the individual and country levels, independent of volume of drinking. In addition, a significant interaction effect indicated that the more detrimental the country's drinking pattern, the less steep the association between the volume of drinking and its consequences. CONCLUSION: Drinking patterns have an independent impact on consequences over and above the relationship between volume and consequences.