medna-metadata: an open-source data management system for tracking environmental DNA samples and metadata.

MOTIVATION: Environmental DNA (eDNA), as a rapidly expanding research field, stands to benefit from shared resources including sampling protocols, study designs, discovered sequences, and taxonomic assignments to sequences. High-quality community shareable eDNA resources rely heavily on comprehensive metadata documentation that captures the complex workflows covering field sampling, molecular biology lab work, and bioinformatic analyses. There are limited sources that provide documentation of database development on comprehensive metadata for eDNA and these workflows and no open-source software. RESULTS: We present medna-metadata, an open-source, modular system that aligns with Findable, Accessible, Interoperable, and Reusable guiding principles that support scholarly data reuse and the database and application development of a standardized metadata collection structure that encapsulates critical aspects of field data collection, wet lab processing, and bioinformatic analysis. Medna-metadata is showcased with metabarcoding data from the Gulf of Maine (Polinski et al., 2019). AVAILABILITY AND IMPLEMENTATION: The source code of the medna-metadata web application is hosted on GitHub (https://github.com/Maine-eDNA/medna-metadata). Medna-metadata is a docker-compose installable package. Documentation can be found at https://medna-metadata.readthedocs.io/en/latest/?badge=latest. The application is implemented in Python, PostgreSQL and PostGIS, RabbitMQ, and NGINX, with all major browsers supported. A demo can be found at https://demo.metadata.maine-edna.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Morphometric study of the anteroventral cochlear nucleus of two mouse models of presbycusis.

The dimensions and volume of the anterior ventral cochlear nucleus (AVCN), the density and number of AVCN neurons, and the size of neuronal somata nuclei (in Nissl-stained tissue) were determined in two mouse models of age-related hearing loss: the C57BL/6J strain, which undergoes progressive chronic sensorineural hearing loss with onset during young adulthood, and the CBA/J, which demonstrates only moderate hearing loss with onset late in life. Frontal and horizontal AVCN sections, as well as cochleas, were analyzed in 4 C57 age-groups (1, 7, 12, 19+ months) and in 3 CBA groups (1, 10, 22 months). Within each strain no significant changes in AVCN dimensions or volume occur with aging. In C57 mice, packing density and cell number decrease between 1 and 7 months, but remain stable thereafter, despite chronic severe hearing impairment. CBA mice show a reduction in AVCN cell number and packing density only during the second year of life. In aging C57 mice, the size of spherical and perhaps globular cells increases, whereas the size of multipolar cells tends to decrease slightly. In CBA mice, all three AVCN cell types tend to decrease in size with aging. The early cell loss and cell size increases in C57 mice are most consistent in the dorsal (high frequency) region of the AVCN. Likewise, loss of cochlear spiral ganglion cells is most pronounced in the base of the cochlea, which provides input to this region. The data indicate that aging is associated with rather different central effects, depending on AVCN cell type, cochleotopic organization, genotype, and/or the type of peripheral hearing loss involved. The C57 and CBA AVCNs also differ in several aspects irrespective of age. The volume of AVCN and number of AVCN neurons are significantly greater in C57 mice.

COX-2 selective nonsteroidal anti-Inflammatory drugs: do they really offer any advantages?

Nonsteroidal anti-inflammatory drugs (NSAIDs) are responsible for substantial morbidity and mortality as a result of the complications associated with gastroduodenal ulcers, such as perforation and bleeding. The central mechanism leading to the gastroduodenal toxicity of NSAIDs is their ability to inhibit mucosal prostaglandin synthesis. Recent recognition that there are 2 isoforms of the enzyme cyclooxygenase (COX) responsible for prostaglandin synthesis has enabled the development of drugs capable of sparing the gastric mucosa. The inducible COX-2 enzyme is responsible for some aspects of pain and inflammation in arthritis while the constitutive COX-1 enzyme appears responsible for most of the gastro-protective prostaglandin synthesis in the stomach and duodenum. Drugs selective for COX-2 probably act by binding to a pocket in the enzyme that is present in COX-2 but not in COX-1. As a result, drugs that have little or no COX-1 activity across their therapeutic dosage range have been developed. Two drugs that are claimed to be highly selective or specific in their ability to inhibit COX-2, rofecoxib and celecoxib, are now available on prescription in the US and rofecoxib is available in Europe. Short term volunteer studies of 7 days' duration and patient studies of 6 months' duration have shown these drugs to have a level of gastroduodenal injury that is similar or equivalent to that seen with placebo, whereas high rates of damage and ulceration are seen with nonselective NSAIDs. In addition, there appear to have been fewer perforations, clinical ulcers and bleeds in the phase III clinical trials of these agents, compared with nonselective NSAIDS. However, more experience will be needed before this promise can be confirmed. In addition, COX-2 inhibitors share the adverse effects of NSAIDs outside the gastrointestinal tract that are dependent on COX-2 inhibition.

Genetic analysis of isolates of the spotted fever group of rickettsiae belonging to the R. conorii complex.

The cytoplasmic 120 kDa antigen genes of 9 isolates of Rickettsia conorii (RC), 12 isolates of R. africae (RA), and 3 isolates of Israeli tick typhus rickettsiae (ISTT) were compared for restriction fragment length polymorphisms (RFLP) present in portions of the open reading frame amplified by polymerase chain reaction (PCR). Initially, DNAs from 13 species or serotypes of spotted fever group rickettsiae were used to select restriction enzymes (RE) that detected RFLP in gene fragments amplified with primer pairs 483WF/1514R and 764F/3409R. Among the R. conorii complex isolates, Dpn II gave RFLP differentiating all three serotypes. Unique RE patterns were obtained for RC with Bsr I and Hinf I, for RA with Mwo I, Pst I and Ssp I, and for ISTT with Hpa II. While RFLP typing of the 120 kDa gene permitted rapid separation of R. conorii complex isolates into three groups corresponding to the RC, RA, and ISTT rOmp serotypes, additional intragroup genetic variation was also detected in all three serotypes.

Coeliac disease and epilepsy.

Whether there is an association between coeliac disease and epilepsy is uncertain. Recently, a syndrome of coeliac disease, occipital lobe epilepsy and cerebral calcification has been described, mostly in Italy. We measured the prevalence of coeliac disease in patients attending a seizure clinic, and investigated whether cerebral calcification occurred in patients with both coeliac disease and epilepsy. Screening for coeliac disease was by IgA endomysial antibody, measured by indirect immunofluorescence using sections of human umbilical cord. Of 177 patients screened, four patients were positive. All had small-bowel histology typical of coeliac disease. The overall frequency of coeliac disease in this mixed patient sample was 1 in 44. In a control group of 488 pregnant patients, two serum samples were positive (1 in 244). Sixteen patients with both coeliac disease and epilepsy, who had previously attended this hospital, were identified. No patient had cerebral calcification on CT scanning. Coeliac disease appears to occur with increased frequency in patients with epilepsy, and a high index of suspicion should be maintained. Cerebral calcification is not a feature of our patients with epilepsy and coeliac disease, and may be an ethnically-or geographically-restricted finding.

Thrombosis in inflammatory bowel disease: clinical setting, procoagulant profile and factor V Leiden.

Patients with inflammatory bowel disease have an increased frequency of thromboembolism, and microvascular thrombosis has been proposed as a contributory pathogenic factor. The mechanism of enhanced procoagulant activity is not understood. We examined the clinical setting of thromboembolic events in 52 patients with Crohn's disease or ulcerative colitis, and assessed the procoagulant laboratory profile, including Factor V Leiden, in a subset of 20 patients to identify procoagulant risk factors. Patients who developed thrombosis tended to be young; 60% of thrombotic events occurred in patients under 50 years. Multiple thromboembolic episodes occurred in 13% and unusual sites of thrombosis (e.g. intracardiac, cerebral, inominate veins) in 11%. No risk factor was identifiable in 52% of cases and two-thirds of thromboses occurred in an out-patient setting. The mortality rate was 8%. Evidence for inflammatory disease activity was found in only 45% of patients with ulcerative colitis at the time of the thromboembolic event, in contrast to 89% of those with Crohn's disease. Assays for specific coagulation defects were negative in all cases tested (protein S, C were normal in 17/17; anti-thrombin III, anti-phospholipid antibodies and activated protein C resistance were negative in 20/20, and only 1/20 patients was found to be heterozygous for Factor V leiden. Thrombosis in inflammatory bowel disease is important because it occurs in a young population, often in unusual sites, and has a high mortality. The development of thrombosis is related to active inflammatory disease in most patients with Crohn's disease but apparently not in those with ulcerative colitis. Since approximately half of the patients had no other identifiable risk factor, there remains a substantial group of patients with IBD who develop thrombosis for unknown reasons.

Copper(II) Schiff-base complexes and apoglobin stability.

N,N'-Propylene-bis-(N-salicylidene)copper(II) (Cu(Salprn)) explicitly stabilizes apomyoglobin. The optical spectrum of this copper(II) Schiff-base complex of apomyoglobin arises from the electronic excitations of pi *-O-Salprn-->dx2-y2 and N-Salprn-->dx2-y2. Shifts of these transitions with respect to those of the parent complex may be a consequence of hydrophobic solvatochromism or binding of an additional ligand. ESR parameters imply no change in the identity of the first coordination sphere around the copper, while hydrophobic solvatochromism cannot be excluded. Combination of copper(II) Schiff-base complex with apomyoglobin does not inhibit the ability of apomyoglobin to extract hemin from the main component of Glycera dibranchiata hemoglobin. Hemin replaces the copper complex, and the value of the apparent first-order rate constant varies with time. The mechanism involves dissociative and associative interchange pathways. Values of rate constants for transfer of hemin to copper(II) Schiff-base apomyoglobin complex, as well as the change of concentration with time are evaluated.

Leptin regulation of reproductive function and fertility.

Leptin, a 16-KD protein secreted primarily by adipose tissue, was first discovered in the search for a satiety signal. When administered into the brain, leptin depresses appetite. Interestingly, hyperphagic, obese, transgenic mice with leptin deficiency were noted to be reproductively incompetent, and administration of leptin restored their fertility. These pivotal observations led to numerous studies on the site of action of leptin within the hypothalamo-hypophyseal-gonadal axis, and a variety of models have been used ranging from the prepubertal condition to fasting suppression of reproductive hormones. The preponderance of studies thus far has focused on how leptin serves as a metabolic signal of energy balance within the neuroendocrine system, particularly as a regulator of GnRH/LH secretion. Less research has been conducted with other components of the reproductive system, but local effects of leptin have been demonstrated in the gonads where hyperleptinemia suppresses steroidogenesis and potentially affects gamete maturation. This presentation will review the major concepts for the role of leptin in the modulation of fertility and will consider the potential use of leptin in assisted reproductive technology and embryo transfer.

Social identity and the true believer: responses to threatened self-stereotypes among the intrinsically religious.

That religion is an impactful social category has often been assumed but seldom tested. Based on social identity and self-categorization theories, it is argued that devout religious commitment reflects, at least in part, an individual's motivation to engage in religious self-stereotyping (i.e. to perceive oneself as an exemplary religious group member). In order to test this analysis, individuals scoring high or low on a measure of intrinsic religious orientation received false feedback that either threatened or bolstered their self-perceptions on a dimension of behaviour that was either important or not important to religious group membership. As expected, intrinsic orientation predicted increased religious self-stereotyping only when feedback was threatening and important to religious group membership; affective and behavioural indices revealed a similar pattern. Implications for the social identity/self-categorization literature, and for theory development in the psychology of religion, are subsequently discussed.

Appropriateness of laboratory tests: requests for atypical pneumonia serology in a teaching hospital.

The cost of providing medical care is ever-increasing but the resources available are at best static. Major savings can be made by reducing inappropriate investigations. Using serological testing for organisms causing atypical pneumonia as an example, we examined the appropriateness of requests and also physicians' understanding of the test. Of 119 patients tested, only 3 had titres indicative of acute infection. Most patients were tested within 2 days of hospital admission, before receipt of results excluding more likely diagnoses. Forty-five patients had no current or recent respiratory symptoms, in whom infection was highly unlikely. Titres were most often requested by the least experienced members of the clinical team. Of 70 patients with an acute illness in whom a definitive diagnosis, bacteriological or otherwise, was not made, in only 9 was a convalescent specimen sent for follow-up titres. Most requests for serology for organisms causing atypical pneumonia were inappropriate. Furthermore, in the majority of cases the test was incorrectly used.

Artifact in the hypnosis-creativity relationship.

Subjects who pretested high or low in hypnotic suggestibility took a creativity test either under hypnosis or in a waking state. All subjects made a global estimate of their general degree of creativity. Greater figural-spatial creativity was exhibited in the hypnosis condition than in the waking condition by both high and low suggestibles. Creativity self-reports were not corroborated by actual creative performance.

Pandemic H1N1 Influenza Infection and Vaccination in Humans Induces Cross-Protective Antibodies that Target the Hemagglutinin Stem.

Most monoclonal antibodies (mAbs) generated from humans infected or vaccinated with the 2009 pandemic H1N1 (pdmH1N1) influenza virus targeted the hemagglutinin (HA) stem. These anti-HA stem mAbs mostly used IGHV1-69 and bound readily to epitopes on the conventional seasonal influenza and pdmH1N1 vaccines. The anti-HA stem mAbs neutralized pdmH1N1, seasonal influenza H1N1 and avian H5N1 influenza viruses by inhibiting HA-mediated fusion of membranes and protected against and treated heterologous lethal infections in mice with H5N1 influenza virus. This demonstrated that therapeutic mAbs could be generated a few months after the new virus emerged. Human immunization with the pdmH1N1 vaccine induced circulating antibodies that when passively transferred, protected mice from lethal, heterologous H5N1 influenza infections. We observed that the dominant heterosubtypic antibody response against the HA stem correlated with the relative absence of memory B cells against the HA head of pdmH1N1, thus enabling the rare heterosubtypic memory B cells induced by seasonal influenza and specific for conserved sites on the HA stem to compete for T-cell help. These results support the notion that broadly protective antibodies against influenza would be induced by successive vaccination with conventional influenza vaccines based on subtypes of HA in viruses not circulating in humans.

Novel concepts about normal sexual differentiation of reproductive neuroendocrine function and the developmental origins of female reproductive dysfunction: the sheep model.

The neuroendocrine regulation of GnRH secretion plays a central role in timing gamete release in both sexes. This regulation is more complex in the female because the discontinuous release of ova is more complex than the continuous release of spermatozoa. This review provides an evolving understanding of the sex differences in reproductive neuroendocrine controls and how these differences arise. The rules for sexual differentiation of steroid feedback control of GnRH secretion conceptually parallel the well-established principles that underlie the sexual differentiation of the internal and external genitalia. In the context of the neuroendocrine regulation of the ovarian cycle, and using the sheep as a model, four steroid feedback controls for GnRH secretion are inherent (default). They require no ovarian developmental input to function appropriately during adulthood. Two steroid feedback controls regulate the preovulatory surge mode of GnRH secretion, and two regulate the pulsatile mode. If the individual is a male, three steroid feedback controls of GnRH secretion become unnecessary or irrelevant, and these are abolished or become functionally inoperative through programmed reductions in hypothalamic sensitivity. This central programming occurs through exposure of presynaptic GnRH neurons in the developing male brain to the androgenic and estrogenic actions of testicular steroids. In precocial species such as ruminants, this programming begins well before birth. Understanding how GnRH secretion normally becomes sexually differentiated is of practical importance to determining how inappropriate hormonal environments during development can variously malprogram the neuroendocrine system to produce a variety of reproductive dysfunctions relating to patterning of gonadotropin secretion.

Hypoglossal neural activity during licking and swallowing in the awake rat.

1. Thirty-five neurons in the hypoglossal nucleus (mXII) of the rat were characterized during licking and swallowing in response to fluid stimulation in an awake, freely moving preparation. Simultaneously recorded electromyographic (EMG) recordings from a subset of oropharyngeal muscles were obtained to delineate both the lick cycle and the occurrence of swallows. Most mXII neurons discharged with rhythmic bursts in phase with licking. Twenty-six of the 35 mXII neurons had bimodal interspike interval (ISI) histograms, reflecting rhythmic bursts and the absence of spontaneous activity. Three mXII cells with unimodal ISI histograms were rhythmically active during licking but had some spontaneous activity. Of the remaining six cells with unimodal ISI histograms, five had nonbursting modes of activity. 2. Phase relationships between neural and EMG activity during licking were determined by cross-correlation and compared with distributions of cross-correlations between lingual and masticatory EMG activity. A bimodal distribution of cross-correlations was obtained by cross-correlating EMG activity between lingual protrudor muscles [genioglossus (GG) or geniohyoid (GH)] and masticatory jaw-opener activity [anterior digastric (AD)] and cross-correlating lingual retractor activity [styloglossus (STY)] with anterior digastric EMG. A similar bimodal distribution of cross-correlations obtained between mXII neuron activity and AD contractions suggested that the majority of mXII neurons (30/35) could be classified as protrudor- or retractor-related. Neurons classified as protrudor-related cells were located ventrally in mXII; cells classified as retractor-related were more dorsally located, consistent with anatomic and physiological descriptions of the myotopic organization of mXII. 3. Ten mXII protrudor-related neurons responded with a mean of 4.9 +/- 2.2 (SD) action potentials per lick cycle and preceded the peak jaw-opening phase of licking by a mean of 22.3 ms. In contrast, the activity of 20 retractor-related mXII neurons lagged the jaw-opening phase of licking by a mean of 55.9 ms, with a mean of 5.5 +/- 3.4 (SD) action potentials occurring per lick cycle. Five other mXII neurons exhibited nonrhythmic activity during licking and could not be classified as protrudor- or retractor-related on the basis of cross-correlations with the AD. 4. The occurrence of a swallow decreased the licking frequency by 21%, corresponding to an increase of approximately 43 ms in the period between AD contractions.(ABSTRACT TRUNCATED AT 400 WORDS)

Vomeronasal organ removal blocks pheromonal induction of estrus in gray short-tailed opossums (Monodelphis domestica).

Estrus is induced in female gray short-tailed opossums (Monodelphis domestica) by exposure to male chemical signals (pheromones). Isolated females remain anestrous, but direct exposure to a male or his scent-marked cage induces estrus within 4-6 days. The objective of this study was to investigate the importance of the vomeronasal organ in detection of and response to estrus-inducing pheromones. The vomeronasal organ was surgically removed through the palate from 8 females (VNX); 5 females (SHAM) underwent sham surgeries in which the vomeronasal organ was exposed but not removed. After a 10-day recovery period, females were placed into male scent-marked cages. Body weight and urogenital sinus cytology were monitored throughout the experiment. All females were anesthetized and perfused with 4% paraformaldehyde 12-13 days after initial pheromone exposure. Vomeronasal organ ablation was evaluated histologically in decalcified snouts. In addition, deafferentation of the accessory olfactory bulb was confirmed by use of a lectin stain specific for the vomeronasal nerve and the glomerular layer of the bulb. All females classified as completely VNX (n = 5) remained anestrous throughout the pheromonal exposure. Incompletely VNX females (n = 2) and all SHAM animals exhibited estrus within 7 days of pheromone stimulation. At perfusion, the mean uterine weight (280.71 +/- 95.6 mg/85 g BW) of SHAM females was greater (p < 0.05) than that of unresponsive, VNX females (133.33 +/- 31.14 mg/85 g). This study demonstrates that the vomeronasal organ is an essential component for transduction of male pheromones required for induction of estrus in a marsupial species.

Evidence for spontaneous postlactational estrus in gray short-tailed opossums (Monodelphis domestica).

Previous studies of the gray short-tailed opossum have shown that ovarian activity and estrus are induced by male pheromones, but we recently documented urogenital sinus (UGS) estrus in postlactational females despite their isolation from the male stimuli known to be associated with induced estrus. Body weights and UGS smears were collected after removal of pups in midlactation (19-37 days postpartum), after weaning (55-61 days postpartum), or after pheromone exposure. Estradiol was measured by RIA in plasma samples collected from dams during lactation, after separation from pups, and at estrus. Average days to UGS estrus from pup removal or initial pheromone exposure differed (P<0.05) only between the midlactation and pheromone exposure groups. Postlactational females showed a decrease in body weight from the time of pup removal or weaning to estrus, which contrasts with the increase seen in pheromonally stimulated females. Plasma estradiol was elevated at estrus in all groups, and females that were paired with males at postlactational estrus mated and produced litters. This study demonstrates that gray short-tailed opossums consistently experience estrus within 2 wk of weaning their young and that postlactational estrus appears to be hormonally and behaviorally equivalent to estrus induced by direct exposure to male pheromones.

Gastrointestinal effects of COX-2 inhibitors.

The developing popularity of non-steroidal anti-inflammatory drugs (NSAIDs) over the last 100 years has been paralleled by an increase in associated complications, particularly affecting the gastrointestinal (GI) tract [1]. Over this period, there have been several attempts to develop less toxic NSAIDs, most of which have been unsuccessful. Since the discovery that the enzyme cyclooxygenase (COX) exists as two isoforms, the largely constitutive COX-1 and the mainly inducible COX-2, much interest has centred on the development of drugs capable of selectively inhibiting COX-2. Early studies that investigated specific COX-2 inhibitors (with no effect on the COX-1 isoform over the whole range of concentrations achieved in clinical usage) are encouraging, as they demonstrate that these drugs have fewer effects on gastroduodenal mucosa than standard NSAIDs given at equivalent doses. Further clinical experience with these agents outside trial settings and additional studies to assess the role of COX-2 when induced in the GI tract are needed, before such agents can be safely recommended for widespread prescribing.

NSAIDs and the GI tract-potential hazards and benefits.

Aspirin and non-aspirin non-steroidal anti-inflammatory drugs (NSAIDs) have a substantial impact upon the gastrointestinal tract with both toxicity and benefit. The major toxicity relates to gastroduodenal ulceration and injury to the small and large intestine. The major benefits relate to evidence that the drugs may prevent, delay or cause regression of progress towards malignancy in the colon, and almost certainly also the stomach. The mechanism of toxicity has been thought to relate to inhibition of the synthesis of prostaglandins, since these are protective to the gastrointestinal mucosa as a result of effects on blood flow and mucus and bicarbonate secretion. It is difficult to attribute any anti-cancer effect to these actions. Promotion of apoptosis, which appears to be independent of prostaglandin synthesis, may better account for both therapeutic benefits and possibly some of the toxicity.

Cyclooxygenase (COX) 1 and 2 in normal, inflamed, and ulcerated human gastric mucosa.

BACKGROUND AND AIMS: Constitutive cyclooxygenase (COX) 1 is believed to mediate prostaglandin dependent gastric protection. However, gastric mucosa contains cells capable of expressing inducible COX-2. We therefore investigated COX-1 and COX-2 expression, localisation, and activity in normal and abnormal human gastric mucosa. METHODS: COX-1 and COX-2 distribution was investigated by light and electron microscopic immunohistochemistry and by western blot analysis, and their contribution to prostaglandin (PG)E(2) synthesis using selective enzyme inhibitors. RESULTS: There was strong parietal cell COX-1 and COX-2 immunoreactivity in all sections and isolated cells, with macrophage and myofibroblast reactivity in some sections. Immunostaining was specifically abolished by antigen absorption. Western blot analysis confirmed COX-1 and 2 expression. COX-1 and COX-2 immunostaining was increased in Helicobacter pylori gastritis, particularly the mid glandular zone and lamina propria inflammatory cells. This was associated with increased ex vivo PGE(2) synthesis (62.4 (13.5) pg/mg v 36.3 (15.5) pg/mg in uninflamed mucosa; p=0. 017) which was significantly inhibited by COX-1 but not COX-2 inhibition. Increased COX-2 immunostaining in macrophages, endothelial cells, and myofibroblasts (with reduced epithelial expression) was seen at the rim of ulcers. CONCLUSION: COX-2, as well as COX-1, is expressed by normal human gastric mucosa and is increased at the rim of ulcers. Although both are increased with H pylori, COX-1 contributes more than COX-2 to gastric PGE(2) production.