From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA.

Spin-Resolved Magneto-Tunneling and Giant Anisotropic g-Factor in Broken Gap InAs-GaSb Core-Shell Nanowires.

We experimentally and computationally investigate the magneto-conductance across the radial heterojunction of InAs-GaSb core-shell nanowires under a magnetic field, B, up to 30 T and at temperatures in the range 4.2-200 K. The observed double-peak negative differential conductance markedly blue-shifts with increasing B. The doublet accounts for spin-polarized currents through the Zeeman split channels of the InAs (GaSb) conduction (valence) band and exhibits strong anisotropy with respect to B orientation and marked temperature dependence. Envelope function approximation and a semiclassical (WKB) approach allow to compute the magnetic quantum states of InAs and GaSb sections of the nanowire and to estimate the B-dependent tunneling current across the broken-gap interface. Disentangling different magneto-transport channels and a thermally activated valence-to-valence band transport current, we extract the g-factor from the spin-up and spin-down dI/dV branch dispersion, revealing a giant, strongly anisotropic g-factor in excess of 60 (100) for the radial (tilted) field configurations.

The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes.

In-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA polymerase II-derived transcripts that are produced from almost any genomic context. Pervasive RNAs are degraded by surveillance mechanisms, but the repertoire of proteins that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and in which initiation and termination of transcription occur at a limited number of sites per chromosome. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. We show here that depletion of RBP33 results in overexpression of ∼40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33-depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.

Lack of autonomy and professional recognition as major factors for burnout in midwives: A systematic mixed-method review.

AIM: The aim of this study was to review the existing evidence on burnout levels in midwives and the main related factors. DESIGN: Mixed studies systematic review. DATA SOURCES: PubMed, Scopus and Web of Science were sourced from 2018 and 2023. REVIEW METHODS: Inclusion criteria: quantitative cross-sectional or qualitative articles published in English within the last 5 years. EXCLUSION CRITERIA: studies with undergraduate or trainee midwives, studies examining the factors in a pandemic setting and those not answering the research question. Potential risk of bias was assessed using the Mixed Methods Assessment Tool (MMAT). A convergent synthesis design was followed through a thematic synthesis using Thomas and Harden's three-step method: inductive coding of the text, development of descriptive themes and generation of analytical themes. Qualitative approaches adopted exploratory descriptive studies and participatory action research. RESULTS: Thirty-six studies were included, with a total of 17,364 participants. There were higher levels of burnout in midwives who were single, under 35-40 years of age, with less than 10 years of experience and those with young children. Stress, anxiety and depression, as well as the emotional impact of traumatic events, have been described as related psychological factors. CONCLUSION: Although extrinsic work factors such as shifts, workload, pay and interpersonal relationships increase burnout, intrinsic factors such as lack of autonomy and recognition are the main factors related to it. IMPACT: What problem did the study address? Burnout among healthcare workers has been recognized as a global crisis requiring urgent attention, specifically in midwives. What were the main findings? There is a persistent shortage of midwives that is attributed in part to chronic retention difficulties related to job burnout expressed by these professionals. Where and on whom will the research have an impact? We seek to address the paucity of research on burnout in midwives in the current crisis in the profession. Work factors such as lack of autonomy or recognition in the profession carry an associated risk of burnout and job attrition. Understanding the factors that contribute to burnout will enable healthcare organizations to reduce the current problem. REPORTING METHOD: PREFERRED: Reporting items for systematic review and meta-analyses (PRISMA). PATIENT OF PUBLIC CONTRIBUTION: No patient or public contribution.

Factors that affect the health of immigrants: Qualitative meta synthesis.

BACKGROUND: Migration has challenged society. Most people who move do so for economic reasons, but others move for more tragic reasons. The proportion of female migrants was slightly higher than that of male migrants, partly due to the longer life expectancy of women and the higher demand for female migrants in care-related Jobs. The process may affect migrants' health, particularly in countries where healthcare is associated with high economic costs or insurance availability. A global systematic review of qualitative studies with meta-synthesis was conducted. The results can be used to support health policy and clinical practice. OBJECTIVE: To describe how migrants perceive and experience the process of migrating and how it affects their health. SEARCH STRATEGY: Databases consulted were Medline, PsychInfo, Cuiden, Cinahl, WOS, Scopus, Social Science Database, and Epistemonikos. Thirty-four articles were selected for final meta-synthesis. INCLUSION CRITERIA: All qualitative primary studies were included that describe the experiences or perceptions of migrants and refugees over 18 years that talk about their migration process and the impact on their health; written in English or Spanish between 2016 and 2021. Articles referring to second generations and those dealing with pathologies that pre-date the migration process were excluded. DATA EXTRACTION AND SYNTHESIS: The COREQ and JBI templates were used as quality criteria. Studies mostly used a phenomenological methodology and in-depth interviews, both individual and group, were used for data collection and narrative synthesis. MAIN RESULTS: Uncertainty emerges as a main category. Three other interrelated themes have a direct impact on migrants' health: Language, Social Networks and Work. There are several conditions in each of these that have a positive or negative impact on health. The gender condition appears in both work and social networks, positively and negatively. DISCUSSION AND CONCLUSIONS: Health would be improved by having a stable job, which would facilitate access to health resources. Social networks and language are facilitators of access to a better job, but not the only condition. From a gender perspective, social networks can become a source of health problems, especially for women. The process of migration places women in a position of vulnerability due to the difficulties of reconciling family and work life. Job insecurity, workload, loss of family life or social isolation increase hopelessness and anxiety, leading to health problems. PUBLIC OR PATIENT CONTRIBUTION: As an academic review study, no patient contribution was required, and this study serves as a theoretical framework for more in-depth research that will work with migrant populations. As a public contribution, this work provides evidence of the need to improve access to health for some populations, in line with the Sustainable Development Goals (SDGs) set for 2030.

Photovoice: An active learning tool with community nursing students.

OBJECTIVE: To assess nursing students' experiences of using photovoice as a pedagogical approach to active learning in the community. METHODS: A descriptive design with a cross-sectional mixed-method questionnaire was used with 108 students following an educational activity, in which their communities were photographed and the impact of the pandemic on vulnerable populations was reflected. Descriptive statistics and thematic analysis were used to analyze the data. RESULTS: Seventy eight percent of the students felt that photovoice was an interesting and useful tool for nurses, 89% affirmed it helped stimulate reflection on social and health inequities in times of pandemic, 82% described that it developed many emotions and feelings and 86% would like to disseminate their photographs directly to stakeholders, citizens, and politicians. Three themes were identified in the data: "stimulate critical reflection", "develop emotional skills", and "encourage action". CONCLUSIONS: Photovoice is a successful active learning pedagogical approach that engages nursing students to develop critical awareness while connecting with their communities, with the real world. It fosters students' sensitivity and motivation and encourages them to take action. Teachers need to introduce new scaffolds for active learning, such as photovoice, to provide innovative academic support that nurtures and develops the next generation of nurses appropriately.

Immunometabolic Profile Associated with Progressive Damage of the Intestinal Mucosa in Adults Screened for Colorectal Cancer: Association with Diet.

Environmental factors such as diet and lifestyle have been shown to influence the development of some intestinal mucosal lesions that may be precursors of colorectal cancer (CRC). The presence of these alterations seems to be associated with misbalanced immunological parameter levels. However, it is still unclear as to which immunological parameters are altered in each phase of CRC development. In this work, we aimed to study the potential relationships of immunological and metabolic parameters with diet in a CRC-related lesion context. Dietary information was obtained using an annual semi-quantitative food-frequency questionnaire (FFQ) from 93 volunteers classified via colonoscopy examination according to the presence of intestinal polyps or adenocarcinoma. Cytokines, chemokines, and adipokines were determined from serum samples. We observed a reduction in adiponectin according to the damage to the mucosa, accompanied by an increase and decrease in C-X-C motif chemokine ligand 10 (CXCL10) and resistin, respectively, in CRC cases. The presence of aberrant crypt foci (ACF) in the polyp group was associated with higher tumor necrosis factor-alpha (TNF-α) concentrations. Vegetables were directly correlated with adiponectin and resistin levels, while the opposite occurred with red meat. A bioactive compound, soluble pectin, showed a negative association with TNF-α. Future dietary strategies could be developed to modulate specific immunological parameters in the context of CRC.

Applying reflective multicriteria decision analysis to understand the value of therapeutic alternatives in the management of gestational and peripartum anaemia in Spain.

BACKGROUND: The objective of the FeminFER project was to assess the value of ferric carboxymaltose following a multicriteria decision analysis in obstetrics and gynaecology in Spain. METHODS: Ferric carboxymaltose (FCM) and ferrous sulphate were evaluated using the EVIDEM framework. Ten stakeholders participated to collect different perspectives. The framework was adapted considering evidence retrieved with a PICO-S search strategy and grey literature. Criteria/subcriteria were weighted by level of relevance and an evidence-based decision-making exercise was developed in each criterion; weights and scores were combined to obtain the value of intervention relative to each criterion/subcriterion, that were further combined into the Modulated Relative Benefit-Risk Balance (MRBRB). RESULTS: The most important criterion favouring FCM was Compared Efficacy/Effectiveness (0.183 ± 0.07), followed by Patient Preferences (0.059 ± 0.10). Only Direct medical costs criterion favoured FS (-0.003 ± 0.03). MRBRB favoured FCM; 0.45 ± 0.19; in a scale from -1 to + 1. CONCLUSIONS: In conclusion, considering the several criteria involved in the decision-making process, participants agreed with the use of FCM according to its MRBRB.

Structural Analysis of the Michael-Michael Ring Closure (MIMIRC) Reaction Products.

A representative number of decalin and hydrindane derivatives 2a-l were prepared in 11-91% yield by means of a cascade reaction of cyclohexanone/cyclopentanone enolates and methyl acrylate through a Michael-Michael ring closure (MIMIRC) process. The relative stereochemistry of the four stereogenic centers formed in all products was determined by analyzing the vicinal coupling constants from the 1H NMR and X-ray crystallography. Such a stereochemical outcome was corroborated by conformational analysis supported by DFT calculations and simulating the 1H NMR spectra of representative products. All products showed the same relative stereochemistry at C-1 and C-8a, while at C-3 and bridgehead carbon C-4a, configurational changes were observed. The present results provide some insights about the scope and limitations of the triple cascade reaction between cycloalkanone enolates with methyl acrylate. This synthetic protocol is still a simple and very practical alternative to generate decalin and hydrindane derivatives with great structural diversity.

Contribution of students to nursing practice settings during clinical training: Design and validation of a questionnaire.

BACKGROUND: A validated questionnaire to measure the contributions of nursing students to clinical settings could potentially assist in the improved management of students in healthcare institutions. AIM: To develop and test the psychometric properties of the questionnaire 'Nursing Student Contributions to Clinical Settings' (CEEEC, Spanish acronym for 'Contribuciones de los Estudiantes de Enfermería a los Entornos Clínicos'). DESIGN: Instrument design and psychometric testing. PARTICIPANTS/SETTINGS: A multicentre study involving 1,098 nursing professionals from three universities and five hospitals of Spain, between January 2019 and March 2020. METHODS: The study was carried out in two phases. Phase 1 involved the questionnaire design by experts (n = 28), which required a review of the available literature, cognitive interviews and Delphi rounds, and a preliminary validity study, which included a pilot test with responses from a sample of nurses (n = 143). Phase 2 involved a formal validation with a wider sample of nurses (n = 927), including factor analysis and a study of convergent validity with the Practice Environment Scale-Nursing Work Index and Health Sciences-Evidence Based Practice. RESULTS: Experts selected 42 items on student contributions. After cognitive interviews, three items were eliminated and seven failed to reach the minimum content validity index (78%). Based on the remaining 32 items, the discrimination index of each item was calculated, and those with <0.3, eight items were sequentially eliminated. The resulting questionnaire contained 24 items grouped into a single factor, which explained 41% of the variance. The internal consistency was excellent (Cronbach's alpha: 0.94), and the convergent validity was confirmed. CONCLUSIONS: A 24-item questionnaire was designed and validated to measure the contributions of nursing students to clinical practice settings. IMPACT: Most hospitals are also teaching centres where nursing students undergo clinical practice. The application of this test will provide insight into the nursing professionals' perception of the students' role.

Exploring The Netley British Red Cross Magazine: An example of the development of nursing and patient care during the First World War.

Netley Hospital played a crucial role in caring for the wounded during the nineteenth century and twentieth century, becoming one of the busiest military hospitals of the time. Simultaneously, Florence Nightingale delved into the concept of health and developed the theoretical basis of nursing. This research aims to describe the experiences related to nursing and patient care described in The Netley British Red Cross Magazine during the First World War. The analysis displays different nurses' roles and the influence of environmental factors in the delivery of the soldiers' care. There are indications that Nightingale's ideas would have infiltrated the nursing practices and other aspects of the soldiers' recovery at Netley. The history of the Netley Red Cross Hospital shows the theoretical and practical advancement of nursing care towards a holistic approach.

Clock Genes Disruption in the Intensive Care Unit.

BACKGROUND: Intensive care unit (ICU) environment disrupts the circadian rhythms due to environmental and other nonphotic synchronizers. The main purpose of this article is to establish whether critically patients have desynchronization at the molecular level after 1 week of stay in the ICU. METHODS: The rhythm of Clock, Bmal1, Cry1, and Per2 genes in neuro-ICU patients (n = 11) on the first day after admission in the unit (1 day) and 1 week later (1 week) was studied, 4 time points throughout the day, at 6, 12, 18, and 24 hours. Human whole blood samples were obtained from neuro-ICU patients. The total RNA was isolated and each sample was reverse transcribed to complementary DNA and quantitative polymerase chain reaction (PCRq) was performed. The possible rhythm was studied using Fourier Series. RESULTS: After 1 week, the clock gene rhythmicity completely disappeared. Messenger RNA (mRNA) expression for the 4 clock genes was shown rhythmicity at the first day after admission in the ICU. Circadian rhythmicity for none of them was observed but rather, ultradian rhythmicity was found. The expression of Clock, Bmal1, and Per2 mRNA after 1 week was similar in the 4-time point studies without significant fluctuation among the 4 time points analyzed. DISCUSSION: Rhythmic mRNA expression is present at the first day after admission in the ICU. However, ICU stay during 1 week affects the molecular machinery of the biological clock generating chronodisruption. Circadian disruption is associated with the risk of several pathologies, thus, it seems to be clear that ICU stay in constant conditions could adversely affect patient evolution and probably, circadian resynchronization restoring clock gene expression could lead to a better clinical evolution of the patient. CONCLUSIONS: Clock genes disruption is observed in neuro-ICU patients. Light therapy as well as melatonin treatment could reduce the impact of ICU stay period in biological clock, thereby improving patients' recovery.

Anomalous pupillary responses to M-cone onsets are linked to ${\rm L}{:}{\rm M}$L:M ratio.

M-cone stimulation induces a pupil constriction to stimulus offset, whereas, with L cones, the pupil responds conventionally with a constriction to onset. To test the possibility that this paradox is linked to the ${\rm L}{:}{\rm M}$L:M ratio, we measured the strength of the effect by injecting a variable amount of positive or negative luminance contamination on either side of M-cone isolation and identifying a balance point at which the pupil responded equally to onset and offset. Nineteen individuals were recruited. In observers with low ${\rm L}{:}{\rm M}$L:M ratio, the paradoxical effect was weak. There was a significant relationship (${{r}^2} = {0.561}$r2=0.561) between the balance point and ${\rm L}{:}{\rm M}$L:M ratio. The effect is likely to be linked to strong inhibitory signals associated with cone-opponent pathways.

Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum.

Human malaria is a devastating disease and a major cause of poverty in resource-limited countries. To develop and adapt within hosts Plasmodium falciparum undergoes drastic switches in gene expression. To identify regulatory regions in the parasite genome, we performed genome-wide profiling of chromatin accessibility in two culture-adapted isogenic subclones at four developmental stages during the intraerythrocytic cycle by using the Assay for Transposase-Accessible Chromatin by sequencing (ATAC-seq). Tn5 transposase hypersensitivity sites (THSSs) localize preferentially at transcriptional start sites (TSSs). Chromatin accessibility by ATAC-seq is predictive of active transcription and of the levels of histone marks H3K9ac and H3K4me3. Our assay allows the identification of novel regulatory regions including TSS and enhancer-like elements. We show that the dynamics in the accessible chromatin profile matches temporal transcription during development. Motif analysis of stage-specific ATAC-seq sites predicts the in vivo binding sites and function of multiple ApiAP2 transcription factors. At last, the alternative expression states of some clonally variant genes (CVGs), including eba, phist, var and clag genes, associate with a differential ATAC-seq signal at their promoters. Altogether, this study identifies genome-wide regulatory regions likely to play an essential function in the developmental transitions and in CVG expression in P. falciparum.

The Recent Evolution of a Maternally-Inherited Endosymbiont of Ticks Led to the Emergence of the Q Fever Pathogen, Coxiella burnetii.

Q fever is a highly infectious disease with a worldwide distribution. Its causative agent, the intracellular bacterium Coxiella burnetii, infects a variety of vertebrate species, including humans. Its evolutionary origin remains almost entirely unknown and uncertainty persists regarding the identity and lifestyle of its ancestors. A few tick species were recently found to harbor maternally-inherited Coxiella-like organisms engaged in symbiotic interactions, but their relationships to the Q fever pathogen remain unclear. Here, we extensively sampled ticks, identifying new and atypical Coxiella strains from 40 of 58 examined species, and used this data to infer the evolutionary processes leading to the emergence of C. burnetii. Phylogenetic analyses of multi-locus typing and whole-genome sequencing data revealed that Coxiella-like organisms represent an ancient and monophyletic group allied to ticks. Remarkably, all known C. burnetii strains originate within this group and are the descendants of a Coxiella-like progenitor hosted by ticks. Using both colony-reared and field-collected gravid females, we further establish the presence of highly efficient maternal transmission of these Coxiella-like organisms in four examined tick species, a pattern coherent with an endosymbiotic lifestyle. Our laboratory culture assays also showed that these Coxiella-like organisms were not amenable to culture in the vertebrate cell environment, suggesting different metabolic requirements compared to C. burnetii. Altogether, this corpus of data demonstrates that C. burnetii recently evolved from an inherited symbiont of ticks which succeeded in infecting vertebrate cells, likely by the acquisition of novel virulence factors.

Slowed dark adaptation in older eyes; effect of location.

PURPOSE: The rate of rod sensitivity recovery following a photobleach is a basic measure of the integrity of the outer retina. Rods are selectively impaired in aging and many disorders of the retina, notably Age-Related Macular Degeneration (AMD). It is not known for certain whether the age-related deficit is a pan-retinal effect or if there are localised regions of impaired rod function. To address this important issue a dual arc stimulus was developed that samples sensitivity recovery in two retinal locations. METHODS: Arc-shaped stimuli were presented on a black CRT screen at two locations, in the inferior visual field. Following a bleach, which was localised to the stimuli, recovery of sensitivity was measured using a modified method of adjustment technique. Neutral density filters were used to extend the luminance range of the CRT. Sensitivity recovery functions were fitted by non-linear regression to a seven-parameter model. RESULTS: Pairs of sensitivity recovery functions were generated from the stimuli. The cone phases of these functions were identical. The slopes of the S2 sections of the curves were steeper for the outer stimuli for both young (p < 0.001) and older (p = 0.003) observers. The difference between the two was the same for the two groups. The α point was reached slightly earlier for the young observers and with the outer stimulus but neither of these effects reached statistical significance. The ß point occurred earlier for the outer stimuli and this effect was statistically significant only for the older group. CONCLUSIONS: The method places minimal demands on observers. The fact that rod sensitivity recovery is slowed in the older normal eye to the same extent in the two locations suggests that this deficit may be uniform across the retina. As there are localised losses in scotopic function in AMD, the technique is ideally suited to distinguishing impaired recovery dynamics due to normal ageing from those caused by disease.

Effects of Estrogen and Phytoestrogen Treatment on an In Vitro Model of Recurrent Stroke on HT22 Neuronal Cell Line.

An increase of stroke incidence occurs in women with the decline of estrogen levels following menopause. This ischemic damage may recur, especially soon after the first insult has occurred. We evaluated the effects of estrogen and phytoestrogen treatment on an in vitro recurrent stroke model using the HT22 neuronal cell line. HT22 cells were treated with 17ß-estradiol or genistein 1 h after the beginning of the first of two oxygen and glucose deprivation/reoxygenation (OGD/R) cycles. During the second OGD, there was a deterioration of some components of the electron transport chain, such as cytochrome c oxidase subunit 1 with a subsequent increase of reactive oxygen species (ROS) production. Accordingly, there was also an increase of apoptotic phenomena demonstrated by poly(ADP-ribose) polymerase 1 cleavage, Caspase-3 activity, and Annexin V levels. The recurrent ischemic injury also raised the hypoxia-inducible factor 1α and glucose transporter 1 levels, as well as the ratio between the lipidated and cytosolic forms of microtubule-associated protein 1A/1B-light chain 3 (LC3-II/LC3-I). We found a positive effect of estradiol and genistein treatment by partially preserving the impaired cell viability after the recurrent ischemic injury; however, this positive effect does not seem to be mediated neither by blocking apoptosis processes nor by decreasing ROS production. This work contribute to the better understanding of the molecular mechanisms triggered by recurrent ischemic damage in neuronal cells and, therefore, could help with the development of an effective treatment to minimize the consequences of this pathology.

Patterns of diversification in islands: A comparative study across three gecko genera in the Socotra Archipelago.

In this study we used the complete fauna of geckos of the Socotra Archipelago to test whether the three gecko genera co-occurring in the islands (Pristurus, Hemidactylus and Haemodracon) produced similar outcomes of morphological and climatic diversification. To test this, we produced a time-calibrated tree of 346 geckos including all 16 endemic species of the archipelago and 26 potential close-relatives in the continent. Our dating estimates revealed that most of the diversity of geckos in the archipelago was the consequence of in situ diversification. However not all genera shared similar patterns of diversification. While in Hemidactylus and Haemodracon this involved great differences in body size and low levels of climatic diversification (mostly involving sympatric distributions), an opposite pattern appeared in Pristurus in which most of the diversification involved shifts in climatic envelopes (mostly involving allopatric and parapatric distributions) but almost no size differentiation. Consistently with this, Pristurus was the only genus in which rates of size diversification in islands were substantially lower than in the continent. This illustrates how different groups can greatly differ in their patterns of intra-island diversification and highlights the importance of taxon-dependent factors at determining different patterns of diversification in the same insular context.

Assessing the diversity, host-specificity and infection patterns of apicomplexan parasites in reptiles from Oman, Arabia.

Understanding the processes that shape parasite diversification, their distribution and abundance provides valuable information on the dynamics and evolution of disease. In this study, we assessed the diversity, distribution, host-specificity and infection patterns of apicomplexan parasites in amphibians and reptiles from Oman, Arabia. Using a quantitative PCR approach we detected three apicomplexan parasites (haemogregarines, lankesterellids and sarcocystids). A total of 13 haemogregarine haplotypes were identified, which fell into four main clades in a phylogenetic framework. Phylogenetic analysis of six new lankesterellid haplotypes revealed that these parasites were distinct from, but phylogenetically related to, known Lankesterella species and might represent new taxa. The percentage of infected hosts (prevalence) and the number of haemogregarines in the blood (parasitaemia) varied significantly between gecko species. We also found significant differences in parasitaemia between haemogregarine parasite lineages (defined by phylogenetic clustering of haplotypes), suggesting differences in host-parasite compatibility between these lineages. For Pristurus rupestris, we found significant differences in haemogregarine prevalence between geographical areas. Our results suggest that host ecology and host relatedness may influence haemogregarine distributions and, more generally, highlight the importance of screening wild hosts from remote regions to provide new insights into parasite diversity.

Staging Lymphadenectomy in Patients With Clear Cell Carcinoma of the Ovary.

OBJECTIVE: The purpose of this study was to assess the rate of lymph node (LN) metastasis in comprehensively staged ovarian clear cell carcinoma (OCCC) clinically confined to the ovary and determine factors associated with LN metastasis. METHODS: We identified all cases of OCCC treated at 4 institutions from January 1994 through December 2011. We included cases with disease grossly confined to the ovary that had surgical staging performed, including at least 10 LNs sampled. Clinical and pathologic data were abstracted from electronic medical records, and a deidentified data set was compiled and processed at a single institution. Factors potentially associated with LN metastasis were tested. Appropriate statistical tests were performed. RESULTS: We identified 145 eligible cases that met the criteria for this analysis. Median age was 52.9 years (range, 30-81 years), and median total LN count was 19 (range, 10-74). Seven (4.8%) of 145 comprehensively staged cases had LN metastasis; 6 of these cases (4.1%) were isolated metastasis. Cytologic washings, peritoneal, omental, and fallopian tube involvement were not associated with nodal metastasis. Cases with ovarian surface involvement and positive cytology had a 37.5% incidence of LN positivity, which was statistically meaningful when compared with all other cases (P = 0.003). CONCLUSIONS: Women who underwent comprehensive staging for clinical stage I OCCC had an LN metastasis rate of 4.8%. The subgroup of cases with both ovarian surface involvement and positive cytology had the highest incidence of LN metastasis. This may influence clinical decision making on whether to perform lymphadenectomy in patients with incidental OCCC found after salpingo-oophorectomy.