3D intrusions transport active surface microbial assemblages to the dark ocean

Subtropical oceans contribute significantly to global primary production, but the fate of the picophytoplankton that dominate in these low-nutrient regions is poorly understood. Working in the subtropical Mediterranean, we demonstrate that subduction of water at ocean fronts generates 3D intrusions with uncharacteristically high carbon, chlorophyll, and oxygen that extend below the sunlit photic zone into the dark ocean. These contain fresh picophytoplankton assemblages that resemble the photic-zone regions where the water originated. Intrusions propagate depth-dependent seasonal variations in microbial assemblages into the ocean interior. Strikingly, the intrusions included dominant biomass contributions from nonphotosynthetic bacteria and enrichment of enigmatic heterotrophic bacterial lineages. Thus, the intrusions not only deliver material that differs in composition and nutritional character from sinking detrital particles, but also drive shifts in bacterial community composition, organic matter processing, and interactions between surface and deep communities. Modeling efforts paired with global observations demonstrate that subduction can flux similar magnitudes of particulate organic carbon as sinking export, but is not accounted for in current export estimates and carbon cycle models. Intrusions formed by subduction are a particularly important mechanism for enhancing connectivity between surface and upper mesopelagic ecosystems in stratified subtropical ocean environments that are expanding due to the warming climate.

Are monoclonals the only panacea for treatment of aquaporin-4 positive NMOSD? Experience from a low-&middle-income (LMIC) region

OBJECTIVE

A plethora of monoclonals have ushered up for NMOSD treatment. However, their limited availability and cost concerns poses a challenge for usage in developing nations. We compared relapse rates and disabilities among aquaporin-4 positive(AQP4+ve) patients on conventional immunosuppressants and rituximab in a tertiary referral center in southern India.

METHODS

This was a chart review of AQP4+ve patients registered under national demyelination registry maintained at institute. AQP4+ve patients were included if they were on azathioprine, MMF, methotrexate for six months; cyclophosphamide for three months and rituximab for one month.

RESULTS

207 records were screened, 154 fulfilled inclusion criteria. Drugs used were azathioprine (70), MMF (34) and rituximab (33). All three drugs were non-inferior to each other in terms of ARR reduction. Median EDSS at last follow-up was significantly lower for azathioprine(2;IQR:0-5) and rituximab(2;IQR:0.5-5) than MMF(3.5;IQR:2-5.6), however azathioprine was associated with highest switch rate(34.3%) and was the only drug which required change because of intolerance. Failure rate was least for rituximab(27.3%).Patients on azathioprine and MMF required higher mean duration of concurrent steroids(7.8±7.7 and 4.56±2.17 months respectively) when compared to rituximab(2.77±1.38) and had more relapses due to steroid withdrawal.

CONCLUSION

Initial treatment with azathioprine, MMF and rituximab is comparable in terms of ARR reduction. Findings suggest that choice may be guided by adverse event profile of drug, rather than efficacy per se. Concurrent treatment duration with steroids should also guide clinical decision. Switch to second immunomodulation in event of initial failure adds to efficacy benefit, irrespective of the drug chosen.

A single Prochlorococcus ecotype dominates the tropical Bay of Bengal with ultradian growth

The Bay of Bengal (BoB) spans >2.2 million km2 in the northeastern Indian Ocean and is bordered by dense populations that depend upon its resources. Over recent decades, a shift from larger phytoplankton to picoplankton has been reported, yet the abundance, activity, and composition of primary producer communities are not well-characterized. We analysed the BoB regions during the summer monsoon. Prochlorococcus ranged up to 3.14 × 105 cells mL-1 in the surface mixed layer, averaging 1.74 ± 0.46 × 105 in the upper 10 m and consistently higher than Synechococcus and eukaryotic phytoplankton. V1-V2 rRNA gene amplicon analyses showed the High Light II (HLII) ecotype formed 98 ± 1% of Prochlorococcus amplicons in surface waters, comprising six oligotypes, with the dominant oligotype accounting for 65 ± 4% of HLII. Diel sampling of a coherent water mass demonstrated evening onset of cell division and rapid Prochlorococcus growth between 1.5 and 3.1 div day-1, based on cell cycle analysis, as confirmed by abundance-based estimates of 2.1 div day-1. Accumulation of Prochlorococcus produced by ultradian growth was restricted by high loss rates. Alongside prior Arabian Sea and tropical Atlantic rates, our results indicate Prochlorococcus growth rates should be reevaluated with greater attention to latitudinal zones and influences on contributions to global primary production.

Cerebrospinal fluid inflammatory cytokine profiles of patients with neurotropic parasitic infections

The pathogenesis of chronic parasitic central nervous system (CNS) infections, including granulomatous amoebic meningoencephalitis (GAE), cerebral toxoplasmosis (CT), and neurocysticercosis (NCC), is primarily due to an inflammatory host reaction to the parasite. Inflammatory cytokines produced by invading T cells, monocytes, and CNS resident cells lead to neuroinflammation which underlie the immunopathology of these infections. Immune molecules, especially cytokines, can therefore emerge as potential biomarker(s) of CNS parasitic infections. In this study, cerebral spinal fluid (CSF) samples from suspected patients with parasitic infections were screened for pathogenic free-living amoebae by culture (n=2506) and PCR (n=275). Six proinflammatory cytokines in smear and culture-negative CSF samples from patients with GAE (n = 2), NCC (n = 7), and CT (n = 23) as well as control (n = 7) patients were measured using the Multiplex Suspension assay. None of the CSF samples tested was positive for neurotropic free-living amoebae by culture and only two samples showed Acanthamoeba 18S rRNA by PCR. Of the six cytokines measured, only IL-6 and IL-8 were significantly increased in all three infection groups compared to the control group. In addition, TNFa levels were higher in the GAE and NCC groups and IL-17 in the GAE group compared to controls. The levels of IL-1b and IFNg were very low in all the infection groups and the control group. There was a correlation between CSF cellularity and increased levels of IL-6, IL-8, and TNFa in 11 patients. Thus, quantifying inflammatory cytokine levels in CSF might help with understanding the level of neuroinflammation in patients with neurotropic parasitic diseases. Further studies with clinico-microbiological correlation in the form of reduction of cytokine levels with treatment and the correlation with neurological deficits are needed.

The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients

The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29°C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 ± 4.4 × 104  cells ml-1 , predominantly HLII, whereas LLII and 'rare' ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 ± 2.3 × 104  cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 × 104  cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto 'rare' picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.

Radiation-Induced Brachial Plexopathy (RIBP) after Stereotactic Body Radiotherapy (SBRT): Pooled Analyses of Risks

PURPOSE/OBJECTIVE(S)

RIBP, with symptomatic upper extremity motor or sensory deficits, is a risk after SBRT. We herein model dosimetric factors associated with risks of RIBP of the inferior aspect of the brachial plexus following SBRT for apical lung tumors.

MATERIALS/METHODS

Literature searches (PubMed & Embase databases) were performed to identify reports published from 2000-2021, using search criteria of ["brachial plex*" and stereotactic]. From a PRISMA systematic review, studies were identified that included individual patient data on: (1) RIBP endpoints after SBRT for apical lung tumors; and (2) brachial plexus Dmax, or maximum point doses (i.e., D0.035cc or D0.03cc). These data were amenable to normal tissue complication probability (NTCP) modelling. Doses were converted using the linear-quadratic model with an alpha-beta ratio of 3 Gy. For the probit models, the parameter values were determined using the maximum likelihood method and the 95% confidence intervals (CI) were determined using the profile likelihood method. The ability of the NTCP models to distinguish patients with and without RIBP was evaluated using the area under the curve (AUC).

RESULTS

Two probit NTCP models were derived: one from 3 studies (185 patients with 192 targets and 11 events) and another from 4 studies (221 patients with 229 targets and 18 events). NTCP models (summarized in table) suggest ≈10% risks associated with brachial plexus maximum dose (Dmax) of ∼32-34 Gy in 3 fractions and ∼40-43 Gy in 5 fractions, with a clear dose response. These dose-responses with SBRT (with steep dose gradients beyond the target volume and thus only partial-irradiation of the brachial plexus) are far less steep than those reported following conventionally-fractionated or moderately-hypofractionated radiotherapy used for breast, lung and head and neck cancers (that tend to use radiotherapy fields that circumferentially irradiate the brachial plexus).

CONCLUSION

A dose-response for risk of RIBP after SBRT is observed relative to brachial plexus Dmax. The less-steep dose-response compared to that seen from conventionally-fractionated or moderately-hypofractionated radiotherapy (with large irradiated plexus volumes) suggest a possible volume dependence of RIBP risks. Future work should focus on understanding possible volume effects.

Multifocal MRI-Directed Simultaneous Integrated Boost (SIB) in the Treatment of Prostate Cancer with Stereotactic Body Radiation Therapy (SBRT)

PURPOSE/OBJECTIVE(S)

Conventionally fractionated MRI-directed radiation boosts in the treatment of prostate cancer have been shown to improve oncologic outcomes in the FLAME trial. Moreover, recent data has demonstrated local recurrences following SBRT predominately occur at the site of the dominant intraprostatic lesion. Modern protocols including HYPO-Flame have demonstrated early safety profiles of a 5-fraction intraprostatic SBRT boost. This study aims to determine if multifocal SIB treatment is associated with additional acute toxicity relative to unifocal boosts.

MATERIALS/METHODS

In this single-center retrospective analysis, we identified all patients who underwent SBRT with a SIB using a robotic radiosurgical platform. Fiducial markers and hydrogel rectal spacers were placed prior to simulation. All patients underwent treatment planning MRI with documented PI-RADS 3-5 lesions targeted for SIB delineation. Patients were treated to a prescription dose of 3500 to 3625 cGy in 5 fractions, or 1800 to 2100 cGy in 3 fractions in concert with pelvic nodal irradiation. The SIB prescription dose ranged from 4000 to 4200 cGy and 2100 to 2300 cGy for the 5- and 3-fraction regimens, respectively. Acute toxicity was defined as that occurring within 60 days of treatment completion using the CTCAE v. 5.0.

RESULTS

A total of 35 patients with a median age of 70 underwent SBRT SIB from 5/2022 to 1/2023 with the following risk distribution: low (3%), intermediate (66%), high (28%), and regional (3%). Most patients received rectal spacers (77%) and neoadjuvant ADT (71%) prior to treatment. The majority of patients underwent 5-fraction SBRT (74%) with the remainder receiving SBRT as a boost. Approximately half (51%) of the cohort was treated with a multifocal SIB to multiple PI-RADS lesions. Mean SIB dose was 4105 and 2377 cGy in 5- and 3-fractions, respectively. With a median follow up of 33 days, we identified no grade 3+ acute toxicities. Crude rate of grade 2 GU and GI toxicity was 51% and 6%, respectively, on par with prior unifocal publications. There was no difference in median SIB volume between uni- and multifocal boosts (1.47 vs. 1.72 cc, p = 0.57), nor was SIB volume associated with an increased risk of grade 2 GU toxicity (p = 0.28). Dominant lesion location was not associated with increased grade 2 GU toxicity (p = 0.29). No grade 2 GI toxicities occurred in the multifocal group. Finally, univariate analysis did not identify multifocal boost as a risk of grade 2 GU toxicity (35%) relative to unifocal (67%) boost (p = 0.09).

CONCLUSION

In the first analysis of its kind in the literature, we demonstrate that multifocal MRI-directed intraprostatic SBRT SIB yields no acute high-grade toxicity and is not associated with a higher risk of low-grade GU and GI toxicity relative to unifocal boost. Longer follow is necessary to determine risk of late toxicity and oncologic efficacy.

5-Year Renal Function Outcomes after SABR for Primary Renal Cell Carcinoma: A Report from the International Radiosurgery Oncology Consortium of the Kidney (IROCK)

PURPOSE/OBJECTIVE(S)

Renal cell carcinoma (RCC) presents uncommonly in patients with a congenital solitary kidney or prior contralateral nephrectomy. The objective of this study was to compare renal function outcomes of stereotactic ablative body radiotherapy (SABR) in patients with solitary vs. bilateral kidneys.

MATERIALS/METHODS

Patients with primary RCC with ≥2 years of follow-up at 12 participating International Radiosurgery Consortium for Kidney (IROCK) institutions were included. Patients with upper tract urothelial carcinoma or metastatic disease were excluded. Renal function was measured by estimated glomerular filtration rate (eGFR). For patients where eGFR was not recorded, Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation was used to estimate eGFR based on known creatinine. Baseline characteristics and renal function outcomes were compared between solitary vs. bilateral kidneys. Multivariable logistic regression was used to identify factors predictive of eGFR decline ≥ 15 mL/min and any eGFR increase evaluated at 1-year post-SABR.

RESULTS

One hundred and ninety patients with solitary (n = 56) or bilateral kidneys (n = 134) underwent SABR and were followed for a median of 5.0 years (IQR: 3.4-6.8). Pre-SABR eGFR (mean ± SD) was similar in patients with solitary (61.1 ± 23.2 mL/min) vs. bilateral kidneys (58.0 ± 22.3 mL/min, p = 0.324). Mean tumor size was 3.70 ± 1.40 cm in solitary and 4.35 ± 2.50 cm in bilateral kidneys (p = 0.026). After SABR, an initial compensatory increase in eGFR was observed in both cohorts (22.7% solitary and 17.7% bilateral at 1 year). This compensatory increase persisted in patients with bilateral but not a solitary kidney (10.3% vs. 0% at 3-years and 21.1% vs. 0% at 5-years, respectively). At 5-years post-SABR, eGFR decreased by -14.5 ± 7.6 in solitary and -13.3 ± 15.9 mL/min in bilateral kidneys (p = 0.665). At all timepoints assessed, there were no significant differences in eGFR decline between solitary vs. bilateral cohorts (all p > 0.05). There were also no significant differences in post-SABR end-stage renal disease (7.1% vs. 6.7%) or dialysis (3.6% vs. 3.7%) in solitary vs. bilateral, respectively. Multivariable analysis demonstrated that increasing tumor size (OR per 1 cm: 1.57; 95% CI: 1.14-2.16, p = 0.006) and baseline eGFR (OR per 10 mL/min: 1.30; 95% CI: 1.02-1.66, p = 0.034) was more likely to be associated with eGFR decline ≥ 15 mL/min. There was no significant association between solitary vs. bilateral kidney and eGFR decline (OR: 1.22; 95% CI: 0.45-3.34, p = 0.693).

CONCLUSION

There was no observed difference between renal function outcomes in patients with a solitary vs. bilateral kidneys. While larger tumor size may increase the risk of eGFR decline post-SABR, treatment of a solitary kidney does not appear to increase the risk of renal dysfunction long-term.

The Southern Ocean mixed layer and its boundary fluxes: fine-scale observational progress and future research priorities

Interactions between the upper ocean and air-ice-ocean fluxes in the Southern Ocean play a critical role in global climate by impacting the overturning circulation and oceanic heat and carbon uptake. Remote and challenging conditions have led to sparse observational coverage, while ongoing field programmes often fail to collect sufficient information in the right place or at the time-space scales required to constrain the variability occurring in the coupled ocean-atmosphere system. Only within the last 10 years have we been able to directly observe and assess the role of the fine-scale ocean and rapidly evolving atmospheric marine boundary layer on the upper limb of the Southern Ocean's overturning circulation. This review summarizes advances in mechanistic understanding, arising in part from observational programmes using autonomous platforms, of the fine-scale processes (1-100 km, hours-seasons) influencing the Southern Ocean mixed layer and its variability. We also review progress in observing the ocean interior connections and the coupled interactions between the ocean, atmosphere and cryosphere that moderate air-sea fluxes of heat and carbon. Most examples provided are for the ice-free Southern Ocean, while major challenges remain for observing the ice-covered ocean. We attempt to elucidate contemporary research gaps and ongoing/future efforts needed to address them. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.

Identification of microbial agents in culture-negative brain abscess samples by 16S/18S rRNA gene PCR and sequencing

Despite clinical suspicion of an infection, brain abscess samples are often culture-negative in routine microbiological testing. Direct PCR of such samples enables the identification of microbes that may be fastidious, non-viable, or unculturable. Brain abscess samples (n = 217) from neurosurgical patients were subjected to broad range 16S rRNA gene PCR and sequencing for bacteria. All these samples and seven formalin-fixed paraffin-embedded tissue (FFPE) samples were subjected to species-specific 18S rRNA PCR for neurotropic free-living amoeba that harbour pathogenic bacteria. The concordance between smear and/or culture and PCR was 69%. One-third of the samples were smear- and culture-negative for bacterial agents. However, 88% of these culture-negative samples showed the presence of bacterial 16S rRNA by PCR. Sanger sequencing of 27 selected samples showed anaerobic/fastidious gram negative bacteria (GNB, 38%), facultative Streptococci (35%), and aerobic GNB (27%). Targeted metagenomics sequencing of three samples showed multiple bacterial species, including anaerobic and non-culturable bacteria. One FFPE tissue revealed the presence of Acanthamoeba 18S rRNA. None of the frozen brain abscess samples tested was positive for 18S rRNA of Acanthamoeba or Balamuthia mandrillaris. The microbial 16/18S rRNA PCR and sequencing outperformed culture in detecting anaerobes, facultative Streptococci and FLA in brain abscess samples. Genetic analyses of 16S/18S sequences, either through Sanger or metagenomic sequencing, will be an essential diagnostic technology to be included for diagnosing culture-negative brain abscess samples. Characterizing the microbiome of culture-negative brain abscess samples by molecular methods could enable detection and/or treatment of the source of infection.

Assessing Changes in Stethoscope Hygiene During COVID-19: A Multicentre Cross-Sectional Study

Background

The COVID-19 (SARS-CoV-2) pandemic has increased infection control vigilance across several modes of patient contact. However, it is unknown whether hygiene pertaining to stethoscopes, which carry the potential for pathogenic contamination, has also shifted accordingly.

Aim

To characterize pandemic-related changes in stethoscope hygiene.

Methods

We surveyed healthcare providers at three major medical centres. Questions quantitatively (Likert scale and frequency) assessed stethoscope hygiene beliefs and practices with two components: before and during COVID-19. Participants were grouped based on performance of optimal stethoscope hygiene (after every patient) before and during COVID-19. Groups were compared using χ² and analysis of variance (ANOVA).

Findings

Of the 515 (10%) who completed the survey, 55 were excluded (N = 460). Optimal hygiene increased from 27.4% to 55.0% (P < 0.001). There were significant increases in Likert scores for all questions pertaining to knowledge of stethoscope contamination (P < 0.001). Belief in stethoscope contamination increased (P < 0.001) despite no change in perceived hygiene education. Resident physicians were less likely compared with attending physicians and nurses to have adopted optimal hygiene during COVID-19 (P < 0.001).

Conclusion

Despite a positive shift in stethoscope hygiene during COVID-19, optimal hygiene was still only performed by around half of providers. Educational interventions, particularly targeting early-career providers, are encouraged.

Central nervous system infections caused by pathogenic free-living amoebae: An Indian perspective

Pathogenic free-living amoebae (FLA), namely Acanthamoeba sp., Naegleria fowleri and Balamuthia mandrillaris are distributed worldwide. These neurotropic amoebae can cause fatal central nervous system (CNS) infections in humans. This review deals with the demographic characteristics, symptoms, diagnosis, and treatment outcomes of patients with CNS infections caused by FLA documented in India. There have been 42, 25, and 4 case reports of Acanthamoeba granulomatous amoebic encephalitis (GAE), N. fowleri primary amoebic meningoencephalitis (PAM), and B. mandrillaris meningoencephalitis (BAE), respectively. Overall, 17% of Acanthamoeba GAE patients and one of the four BAE patients had some form of immunosuppression, and more than half of the N. fowleri PAM cases had history of exposure to freshwater. Acanthamoeba GAE, PAM, and BAE were most commonly seen in males. Fever, headache, vomiting, seizures, and altered sensorium appear to be common symptoms in these patients. Some patients showed multiple lesions with edema, exudates or hydrocephalus in their brain CT/MRI. The cerebrospinal fluid (CSF) of these patients showed elevated protein and WBC levels. Direct microscopy of CSF was positive for amoebic trophozoites in 69% of Acanthamoeba GAE and 96% of PAM patients. One-fourth of the Acanthamoeba GAE and all the BAE patients were diagnosed only by histopathology following autopsy/biopsy samples. Twenty-one Acanthamoeba GAE survivors were treated with cotrimoxazole, rifampicin, and ketoconazole/amphotericin B, and all eleven PAM survivors were treated with amphotericin B alongside other drugs. A thorough search for these organisms in CNS samples is necessary to develop optimum treatment strategies.

A Rare Case of Wobbly, Psychotic Patient with Frozen Eyes - Anti-AMPA Receptor Encephalitis

Background

Anti α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) encephalitis is a rare autoimmune encephalitis. They present with memory, confusion or behavioral changes.

Objective

The aim of this study was to describe unusual clinical features in a patient with AMPAR-associated encephalitis.

Case

A 42-year-old female presented to us with bulbar and gait disturbances of three weeks duration and behavioral changes for ten days. She was found to have memory impairment along with psychosis. She had left eye ptosis, restricted eye movements, sluggish deep tendon reflexes, and bilateral cerebellar signs. Her serum and CSF (cerebrospinal fluid) AMPAR2 antibodies were strongly positive; CT (computed tomography) chest showed evidence of Thymoma. She was treated with steroids with significant improvement initially but expired within 3 months of diagnosis.

Conclusion

This is the first report of AMPAR associated encephalitis from India presenting with unique clinical features affecting both the CNS (central nervous system)--(psychosis, ataxia, cognition) and PNS--peripheral nervous system involvement (ptosis, restricted eye movements, bulbar disturbances).

Flow-Driven Branching in a Frangible Porous Medium

Channel formation and branching is widely seen in physical systems where movement of fluid through a porous structure causes the spatiotemporal evolution of the medium. We provide a simple theoretical framework that embodies this feedback mechanism in a multiphase model for flow through a frangible porous medium with a dynamic permeability. Numerical simulations of the model show the emergence of branched networks whose topology is determined by the geometry of external flow forcing. This allows us to delineate the conditions under which splitting and/or coalescing branched network formation is favored, with potential implications for both understanding and controlling branching in soft frangible media.

Stable aerobic and anaerobic coexistence in anoxic marine zones

Mechanistic description of the transition from aerobic to anaerobic metabolism is necessary for diagnostic and predictive modeling of fixed nitrogen loss in anoxic marine zones (AMZs). In a metabolic model where diverse oxygen- and nitrogen-cycling microbial metabolisms are described by underlying redox chemical reactions, we predict a transition from strictly aerobic to predominantly anaerobic regimes as the outcome of ecological interactions along an oxygen gradient, obviating the need for prescribed critical oxygen concentrations. Competing aerobic and anaerobic metabolisms can coexist in anoxic conditions whether these metabolisms represent obligate or facultative populations. In the coexistence regime, relative rates of aerobic and anaerobic activity are determined by the ratio of oxygen to electron donor supply. The model simulates key characteristics of AMZs, such as the accumulation of nitrite and the sustainability of anammox at higher oxygen concentrations than denitrification, and articulates how microbial biomass concentrations relate to associated water column transformation rates as a function of redox stoichiometry and energetics. Incorporating the metabolic model into an idealized two-dimensional ocean circulation results in a simulated AMZ, in which a secondary chlorophyll maximum emerges from oxygen-limited grazing, and where vertical mixing and dispersal in the oxycline also contribute to metabolic co-occurrence. The modeling approach is mechanistic yet computationally economical and suitable for global change applications.

Newly discovered deep-branching marine plastid lineages are numerically rare but globally distributed

Ocean surface warming is resulting in an expansion of stratified, low-nutrient environments, a process referred to as ocean desertification [1]. A challenge for assessing the impact of these changes is the lack of robust baseline information on the biological communities that carry out marine photosynthesis. Phytoplankton perform half of global biological CO₂ uptake, fuel marine food chains, and include diverse eukaryotic algae that have photosynthetic organelles (plastids) acquired through multiple evolutionary events [1-3]. While amassing data from ocean ecosystems for the Baselines Initiative (6,177 near full-length 16S rRNA gene sequences and 9.4 million high-quality 16S V1-V2 amplicons) we identified two deep-branching plastid lineages based on 16S rRNA gene data. The two lineages have global distributions, but do not correspond to known phytoplankton. How the newly discovered phytoplankton lineages contribute to food chains and vertical carbon export to the deep sea remains unknown, but their prevalence in expanding, low nutrient surface waters suggests they will have a role in future oceans.

Submesoscale-selective compensation of fronts in a salinity-stratified ocean

Salinity, rather than temperature, is the leading influence on density in some regions of the world's upper oceans. In the Bay of Bengal, heavy monsoonal rains and runoff generate strong salinity gradients that define density fronts and stratification in the upper ~50 m. Ship-based observations made in winter reveal that fronts exist over a wide range of length scales, but at O(1)-km scales, horizontal salinity gradients are compensated by temperature to alleviate about half the cross-front density gradient. Using a process study ocean model, we show that scale-selective compensation occurs because of surface cooling. Submesoscale instabilities cause density fronts to slump, enhancing stratification along-front. Specifically for salinity fronts, the surface mixed layer (SML) shoals on the less saline side, correlating sea surface salinity (SSS) with SML depth at O(1)-km scales. When losing heat to the atmosphere, the shallower and less saline SML experiences a larger drop in temperature compared to the adjacent deeper SML on the salty side of the front, thus correlating sea surface temperature (SST) with SSS at the submesoscale. This compensation of submesoscale fronts can diminish their strength and thwart the forward cascade of energy to smaller scales. During winter, salinity fronts that are dynamically submesoscale experience larger temperature drops, appearing in satellite-derived SST as cold filaments. In freshwater-influenced regions, cold filaments can mark surface-trapped layers insulated from deeper nutrient-rich waters, unlike in other regions, where they indicate upwelling of nutrient-rich water and enhanced surface biological productivity.

Is it really possible to predict the consistency of a pituitary adenoma preoperatively?

OBJECTIVES

To determine if the consistency of pituitary adenomas can be predicted based on a preoperative MRI study and to assess the surgical outcome of firm pituitary adenomas.

MATERIALS AND METHODS

One hundred consecutive patients with pituitary adenomas and suprasellar extension were operated by a transsphenoidal approach from July 2003 to December 2006. In addition to the neurological examination, the patients were evaluated by ophthalmological, endocrinological and radiological workups. The signal intensity of the lesion on T2WI and other dimensions of the tumors were included in the MRI study.

RESULTS

There were 52 male and 48 female patients with a mean age of 42.47 years. The mean diameter of the tumor was 32.97mm and the mean SSE was 14.95mm. Six out of 100 patients had firm adenomas peroperatively. Only one of the six patients had isointense SI on T2 WI. Of these 6 patients, total excision was performed in 1 patient, subtotal in 3 patients and partial excision in 2 patients. Among the six patients with firm adenomas, 4 had preoperative hypopituitarism (P<0.001). There was a statistically significant correlation between consistency and the postoperative permanent hypopituitarism (P<0.001). The average follow up was 43.5 months. The literature is reviewed and various aspects of pituitary adenoma consistency are discussed.

CONCLUSIONS

With the present study, the consistency of pituitary adenomas cannot be reliably predicted based on a preoperative MRI study. Patients with firm adenomas likely to have more incidence of preoperative hypopituitarism and postoperative permanent hypopituitarism.

A rare case of multiple brain abscess and probably disseminated phaeohyphomycosis due to Cladophialophora bantiana in an immunosuppressed individual from India

Cladophialophora bantiana, a dematiaceous neurotropic mold causes rare and lethal brain abscess, commonly in immunocompetent hosts. We report a rare and probably a case of disseminated infection with this black mold in an immunosuppressed individual from India. A 55-year-old diabetic male presented with severe headache, blurred-vision, behavioural abnormalities, eye-pain and ear-discharge. He was undergoing treatment for hypertension, prostatomegaly and obstructive pulmonary disease. He was on steroids for the past six years for uveitis. Haematology reports indicated elevated WBC and platelet count. He was negative for HIV, hepatitis, autoimmune antibodies and tumour markers. CD4 count was within normal limits. Brain magnetic resonance imaging revealed multiple ring-enhancing lesions and oedema in the left tempero-parietal region. Chest X-ray showed irregular consolidations in right paracardiac region and confluence in both lungs. Positron Emission Tomography of whole body revealed multiple lesions in brain, lungs, lymph nodes and C3-vertebrae. Histopathology of the lung lesion showed non-tuberculous infectious pathology and brain lesions showed necrosis with occurrence of pigmented hyphal fungi. The pus aspirated during surgical excision of brain lesions grew black mold, identified as C. bantiana. Although patient was started on intravenous Voriconazole, he succumbed to the infection after 7 days. The lesion was initially suspected to be of tuberculous etiology, and the lesions in lungs were also suggestive of malignancy, which was however ruled out by histopathological examination. Such diagnostic dilemmas are common in the infection caused by Cladophialophora, which can cause treatment delay and death. Early diagnosis is therefore mandatory for the rapid treatment and survival of patients.

GAIN: A graphical method to automatically analyze individual neurite outgrowth

BACKGROUND

Neurite outgrowth is a metric widely used to assess the success of in vitro neural stem cell differentiation or neuron reprogramming protocols and to evaluate high-content screening assays for neural regenerative drug discovery. However, neurite measurements are tedious to perform manually, and there is a paucity of freely available, fully automated software to determine neurite measurements and neuron counting. To provide such a tool to the neurobiology, stem cell, cell engineering, and neuroregenerative communities, we developed an algorithm for performing high-throughput neurite analysis in immunofluorescent images.

NEW METHOD

Given an input of paired neuronal nuclear and cytoskeletal microscopy images, the GAIN algorithm calculates neurite length statistics linked to individual cells or clusters of cells. It also provides an estimate of the number of nuclei in clusters of overlapping cells, thereby increasing the accuracy of neurite length statistics for higher confluency cultures. GAIN combines image processing for neuronal cell bodies and neurites with an algorithm for resolving neurite junctions.

RESULTS

GAIN produces a table of neurite lengths from cell body to neurite tip per cell cluster in an image along with a count of cells per cluster.

COMPARISON WITH EXISTING METHODS

GAIN's performance compares favorably with the popular ImageJ plugin NeuriteTracer for counting neurons, and provides the added benefit of assigning neurites to their respective cell bodies.

CONCLUSIONS

In summary, GAIN provides a new tool to improve the robust assessment of neural cells by image-based analysis.

Successful treatment of primary cerebral mucormycosis: Role of microbiologist

Fungal brain abscess is rare with a rapidly progressive disease with fulminant course and invariably fatal outcome, unless diagnosed early and treated rapidly. We report a 56-year-old woman diagnosed to have fungal abscess who recovered completely following amphotericin B treatment. She presented with weakness of the right hand, deviation of mouth to left and aphasia for 2 days. Computed tomography of the brain revealed a left frontal capsuloganglionic hypodense lesion. Stereotactic biopsy was performed, and microbiological confirmation of non-septate fungal hyphae from pus from aspirate within 2 h helped initiate timely and appropriate treatment leading to cure. Histopathology and culture later confirmed mucormycosis.

A genomic case study of mixed fibrolamellar hepatocellular carcinoma

We report the first comprehensive genomic analysis of a case of mixed conventional and fibrolamellar HCC (mFL-HCC). This study confirms the expression of DNAJB1:PRKACA, a fusion previously associated with pure FL-HCC but not conventional HCC, in mFL-HCC. These results indicate the DNAJB1:PRKACA fusion has diagnostic utility for both pure and mixed FL-HCC.

Background

Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been associated with worse prognosis. Recent genomic characterization of pure FL-HCC identified a highly recurrent transcript fusion (DNAJB1:PRKACA) not found in conventional HCC.

Patients and Methods

We performed exome and transcriptome sequencing of a case of mFL-HCC. A novel BAC-capture approach was developed to identify a 400 kb deletion as the underlying genomic mechanism for a DNAJB1:PRKACA fusion in this case. A sensitive Nanostring Elements assay was used to screen for this transcript fusion in a second case of mFL-HCC, 112 additional HCC samples and 44 adjacent non-tumor liver samples.

Results

We report the first comprehensive genomic analysis of a case of mFL-HCC. No common HCC-associated mutations were identified. The very low mutation rate of this case, large number of mostly single-copy, long-range copy number variants, and high expression of ERBB2 were more consistent with previous reports of pure FL-HCC than conventional HCC. In particular, the DNAJB1:PRKACA fusion transcript specifically associated with pure FL-HCC was detected at very high expression levels. Subsequent analysis revealed the presence of this fusion in all primary and metastatic samples, including those with mixed or conventional HCC pathology. A second case of mFL-HCC confirmed our finding that the fusion was detectable in conventional components. An expanded screen identified a third case of fusion-positive HCC, which upon review, also had both conventional and fibrolamellar features. This screen confirmed the absence of the fusion in all conventional HCC and adjacent non-tumor liver samples.

Conclusion

These results indicate that mFL-HCC is similar to pure FL-HCC at the genomic level and the DNAJB1:PRKACA fusion can be used as a diagnostic tool for both pure and mFL-HCC.

The Impact of Submesoscale Physics on Primary Productivity of Plankton

Life in the ocean relies on the photosynthetic production of phytoplankton, which is influenced by the availability of light and nutrients that are modulated by a host of physical processes. Submesoscale processes are particularly relevant to phytoplankton productivity because the timescales on which they act are similar to those of phytoplankton growth. Their dynamics are associated with strong vorticity and strain rates that occur on lateral scales of 0.1-10 km. They can support vertical velocities as large as 100 m d(-1) and play a crucial role in transporting nutrients into the sunlit ocean for phytoplankton production. In regimes with deep surface mixed layers, submesoscale instabilities can cause stratification within days, thereby increasing light exposure for phytoplankton trapped close to the surface. These instabilities help to create and maintain localized environments that favor the growth of phytoplankton, contribute to productivity, and cause enormous heterogeneity in the abundance of phytoplankton, which has implications for interactions within the ecosystem.

Diagnostic Accuracy of PET, SPECT, and Arterial Spin-Labeling in Differentiating Tumor Recurrence from Necrosis in Cerebral Metastasis after Stereotactic Radiosurgery

BACKGROUND AND PURPOSE

Radiographic assessment of cerebral metastasis after stereotactic radiosurgery remains a major challenge in neuro-oncology. It is often difficult to distinguish tumor progression from radiation necrosis in this setting using conventional MR imaging. The objective of this study was to compare the diagnostic sensitivity and specificity of different functional imaging modalities for detecting tumor recurrence after stereotactic radiosurgery.

MATERIALS AND METHODS

We retrospectively reviewed patients treated between 2007 and 2010 and identified 14 patients with cerebral metastasis who had clinical or radiographic progression following stereotactic radiosurgery and were imaged with arterial spin-labeling, FDG-PET, and thallium SPECT before stereotactic biopsy. Diagnostic accuracy, specificity, sensitivity, positive predictive value, and negative predictive value were calculated for each imaging technique by using the pathologic diagnosis as the criterion standard.

RESULTS

Six patients (42%) had tumor progression, while 8 (58%) developed radiation necrosis. FDG-PET and arterial spin-labeling were equally sensitive in detecting tumor progression (83%). However, the specificity of arterial spin-labeling was superior to that of the other modalities (100%, 75%, and 50%, respectively). A combination of modalities did not augment the sensitivity, specificity, positive predictive value, or negative predictive value of arterial spin-labeling.

CONCLUSIONS

In our series, arterial spin-labeling positivity was closely associated with the pathologic diagnosis of tumor progression after stereotactic radiosurgery. Validation of this finding in a large series is warranted.

CPT-11/bevacizumab for the treatment of refractory brain metastases in patients with HER2-neu-positive breast cancer

Nervous system relapse of patients with advanced HER2-neu-positive breast cancer is an increasing problem, with one-third of women developing brain metastases. Standard therapies using steroids, surgery and radiotherapy do not provide a lasting response. We evaluated CPT-11 and bevacizumab, which can both cross the blood-brain barrier, as combination therapy to treat HER2-neu-positive breast cancer with brain metastases.

Biosynthesis of gold nanoparticles and related cytotoxicity evaluation using A549 cells

Biosynthesis of gold nanoparticles (AuNPs) has become an attractive area of research as it is environmentally benign. The toxicity of AuNPs synthesized by chemical routes has been widely studied. However, little is known about the toxicity associated with the biological synthesis of AuNPs. The present study was carried out to synthesize AuNPs using star anise (Illicium verum; a commercially available spice in abundance)and evaluate its toxicity using human epithelial lung cells (A549) in comparison with AuNPs synthesized by the traditional chemical methods (using sodium citrate and sodium borohydride). Apart from cell viability, markers of oxidative stress (reduced glutathione) and cell death (caspases) were also evaluated to understand the mechanisms of toxicity. Cell viability was observed to be 65.7 percent and 72.3 percent in cells exposed to chemically synthesized AuNPs at the highest dose (200nM) as compared to 80.2 percent for biologically synthesized AuNPs. Protective coating/capping of AuNPs by various polyphenolic compounds present in star anise extract appears to be a major contributor to lower toxicity observed in biologically synthesized AuNPs.

Eddy-driven subduction exports particulate organic carbon from the spring bloom

The export of particulate organic carbon (POC) from the surface ocean to depth is traditionally ascribed to sinking. Here, we show that a dynamic eddying flow field subducts surface water with high concentrations of nonsinking POC. Autonomous observations made by gliders during the North Atlantic spring bloom reveal anomalous features at depths of 100 to 350 meters with elevated POC, chlorophyll, oxygen, and temperature-salinity characteristics of surface water. High-resolution modeling reveals that during the spring transition, intrusions of POC-rich surface water descend as coherent, 1- to 10-kilometer-scale filamentous features, often along the perimeter of eddies. Such a submesoscale eddy-driven flux of POC is unresolved in global carbon cycle models but can contribute as much as half of the total springtime export of POC from the highly productive subpolar oceans.

Evolution of MRI changes in Rasmussen's encephalitis

PURPOSE

We studied the MRI findings in 16 patients with Rasmussen's encephalitis (RE), further analysed serial MRI changes in 11 of them and correlated it with clinical features.

METHODOLOGY

The diagnosis of RE was based on the European consensus statement (Brain, 128, 2005, 454). Details related to demographical, clinical, MRI observations were analysed.

RESULTS

Forty MRIs of brain of 16 patients were reviewed. Eleven patients had undergone serial brain MRIs ranging from two to five occasions. All the patients had unihemispheric focal cortical atrophy, predominantly in the perisylvian region (n = 13). Other features were white matter signal changes (n = 14), and ipsilateral caudate (n = 6) and putamen (n = 4) atrophy. Signal alterations in putamen and caudate were noted in four each. In all the 11 patients with serial MRI, there was progression of cerebral atrophy and a trend towards increase in MRI staging. The MRI signal changes remained same in five patients, resolved in three patients, differential change in two patients and increased in one patient. Diffusion-weighted imaging showed facilitated diffusion (n = 5), and MR spectroscopy showed reduced N-acetyl-aspartate and elevated lactate (n = 2).

CONCLUSIONS

Pattern recognition of MRI findings and the changes in serial MRI might serve as a surrogate marker of disease viz. unihemispheric progressive focal cortical atrophy and signal changes predominantly in the perisylvian distribution and caudate followed by putamen involvement. This might assist in understanding and monitoring of the disease progression.

Novel 3-substituted rimonabant analogues lack Δ(9) -tetrahydrocannabinol-like abuse-related behavioural effects in mice

BACKGROUND AND PURPOSE

Previous structure-activity relationship studies with analogues of the CB1 receptor antagonist rimonabant have demonstrated that a subset of these analogues with 3-substituent replacements of rimonabant's pyrazole core displayed cannabimimetic profiles seemingly independent of CB1 receptors. We sought to further evaluate these analogues in several behavioural models sensitive to detecting THC-like abuse liability.

EXPERIMENTAL APPROACH

Selected analogues were tested in a battery of tests in mice to replicate previous findings. Cross-generalization tests were conducted in mice trained to discriminate either THC or O-6629 from vehicle. Rimonabant and its analogues were also evaluated in substitution and challenge tests. Finally, development of cross-tolerance between THC and O-6211 in the mouse test battery was assessed.

KEY RESULTS

O-6629 and O-6658 produced dose-dependent acute cannabimimetic activity in mice, but neither substituted for nor antagonized THC's discriminative stimulus. Cross-substitution was observed with O-6658 in mice discriminating O-6629, whereas rimonabant neither substituted for nor attenuated the O-6629 discriminative stimulus. THC and morphine did not generate O-6629-like responding. Cross-tolerance did not develop in mice repeatedly treated with THC when tested with O-6211 in the mouse test battery.

CONCLUSIONS AND IMPLICATIONS

While some overlap exists between the pharmacological profiles of THC and these 3-substituent rimonabant analogues, the effects are mediated by distinct neural targets. Notably, these analogues are unlikely to possess marijuana-like abuse liability in humans, but general abuse liability has not yet been determined. Efforts to determine the mechanism(s) of action of this seemingly unique class of compounds are underway.

Stereotactic biopsy of brainstem lesions: Techniques, efficacy, safety, and disease variation between adults and children: A single institutional series and review

BACKGROUND

Stereotactic biopsy of brainstem lesions have been performed with varying indications, with most of the literature reporting on children.

MATERIALS AND METHODS

The present study retrospectively analyzed all cases that underwent stereotactic biopsy for brainstem lesion in both adult and pediatric population between 1994 and 2009 in a single tertiary neurosurgical center. The clinical and radiological features, technique of the procedure, morbidity, diagnostic accuracy, spectrum of diagnosis, and variations in adult and pediatric population were analyzed.

RESULTS

Eighty-two patients were included in the study. Computed tomography (CT) was used as guidance in 73 (38 children and 35 adults) patients and magnetic resonance imaging (MRI) in 9 (3 children and 6 adults). The biopsy was performed in a procedure room under local anesthesia in most adults, while children required sedation. Glioblastoma comprised 29.3% of all pathologies in children, compared with only 4.9% of the pathologies in adult population (P = 0.007). Tuberculosis was the next major diagnosis (9.8%). In 12 patients, initial biopsy was inconclusive. Following a repeat biopsy in 5 of these patients, a diagnosis was possible for 75/82 (91.5%) patients by STB. The location of the target, the choice of entry, the radiological characteristic of the lesion, enhancement pattern, and age group did not significantly correlate with the occurrence of inconclusive biopsy. Permanent complications occurred in two patients (2.4%). There was no mortality in this series.

CONCLUSION

Stereotactic biopsy has an important role in brainstem lesions, more significantly in adults, due to wider pathological spectrum. It can be performed safely under local anesthesia through a twist drill craniostomy in most of the adults.