Meta-analysis of yield and nitrous oxide outcomes for nitrogen management in agriculture.

Improved nitrogen (N) use is key to future food security and environmental sustainability. While many regions still experience N shortages, agriculture is the leading global emitter of N2 O due to losses exacerbated by N surpluses in other regions. In order to sustainably maintain or increase food production, farmers and their advisors need a comprehensive and actionable understanding of how nutrient management affects both yield and N2 O emissions, particularly in tropical and subtropical agroecosystems. We performed a meta-analysis to determine the effect of N management and other factors on N2 O emissions, plant N uptake, and yield. Our analysis demonstrates that performance indicators-partial N balance and partial factor productivity-predicted N2 O emissions as well as or better than N rate. While we observed consistent production and environmental benefits with enhanced-efficiency fertilizers, we noted potential trade-offs between yield and N2 O emissions for fertilizer placement. Furthermore, we observed confounding effects due to management dynamics that co-vary with nutrient application practices, thus challenging the interpretation of the effect of specific practices such as fertilization frequency. Therefore, rather than providing universally prescriptive management for N2 O emission reduction, our evidence supports mitigation strategies based upon tailored nutrient management approaches that keep N balances within safe limits, so as to minimize N2 O emissions while still achieving high crop yields. The limited evidence available suggests that these relationships hold for temperate, tropical, and subtropical regions, but given the potential for expansion of N use in crop production, further N2 O data collection should be prioritized in under-represented regions such as Sub-Saharan Africa.

Differentiating Biliary Atresia From Idiopathic Neonatal Hepatitis: A Novel Keratin 7 Based Mathematical Approach on Liver Biopsies.

BACKGROUND AND AIMS: Differentiating biliary atresia (BA) from idiopathic neonatal hepatitis (INH) is vital in routine pediatric practice. However, on liver biopsy, few cases offer a diagnostic challenge to discriminate these entities with certainty. Bile ductular reaction (DR), intermediate hepatobiliary cells (IHBC) and extra-portal ductules (EPD) indicate progenitor cell activation, as a response to various hepatic insults. The present study aims to quantify DR, IHBC and EPD by Keratin 7 (CK7) immunohistochemistry (IHC) in BA and INH and to devise a mathematical approach to better differentiate the two, especially in histologically equivocal cases. METHODS: A total of 98 cases were categorized on biopsy as BA, INH or equivocal histology, favoring BA or INH. CK7 DR mean, IHBC mean and EPD mean values were compared between BA and INH. A formula was derived to help distinguish these two entities, the cut-off value, sensitivity and specificity of which were determined by receiver operating characteristic (ROC) curve. This formula was applied and validated on histologically equivocal cases. RESULTS: Univariate logistic regression revealed significant difference between BA and INH with respect to CK7 DR and CK7 EPD mean (p < 0.001 in both); however, CK7 IHBC mean was not significant (p = 0.08). On multivariate logistic regression, only CK7 DR had significant impact on diagnosis (p < 0.001). A formula: (CK7 DR)2 + (CK7 EPD)/(CK7 IHBC) was derived to help distinguish BA from INH. Cut off value of 10.5 and above, determined by ROC curve, favored a diagnosis of BA (sensitivity= 93.4%, specificity= 94.6%). Histologically equivocal and discrepant cases could be correctly categorized using this formula. CONCLUSIONS: Formula using CK7 IHC parameters may aid pathologists better distinguish BA from INH, especially in histologically equivocal cases.

Multi-faceted impact and outcome of COVID-19 on smallholder agricultural systems: Integrating qualitative research and fuzzy cognitive mapping to explore resilient strategies.

The shock of Coronavirus Disease 2019 (COVID-19) has disrupted food systems worldwide. Such disruption, affecting multiple systems interfaces in smallholder agriculture, is unprecedented and needs to be understood from multi-stakeholder perspectives. The multiple loops of causality in the pathways of impact renders the system outcomes unpredictable. Understanding the nature of such unpredictable pathways is critical to identify present and future systems intervention strategies. Our study aims to explore the multiple pathways of present and future impact created by the pandemic and "Amphan" cyclonic storm on smallholder agricultural systems. Also, we anticipate the behaviour of the systems elements under different realistic scenarios of intervention. We explored the severity and multi-faceted impacts of the pandemic on vulnerable smallholder agricultural production systems through in-depth interactions with key players at the micro-level. It provided contextual information, and revealed critical insights to understand the cascading effect of the pandemic and the cyclone on farm households. We employed thematic analysis of in-depth interviews with multiple stakeholders in Sundarbans areas in eastern India, to identify the present and future systems outcomes caused by the pandemic, and later compounded by "Amphan". The immediate adaptation strategies of the farmers were engaging family labors, exchanging labors with neighbouring farmers, borrowing money from relatives, accessing free food rations, replacing dead livestock, early harvesting, and reclamation of waterbodies. The thematic analysis identified several systems elements, such as harvesting, marketing, labor accessibility, among others, through which the impacts of the pandemic were expressed. Drawing on these outputs, we employed Mental Modeler, a Fuzzy-Logic Cognitive Mapping tool, to develop multi-stakeholder mental models for the smallholder agricultural systems of the region. Analysis of the mental models indicated the centrality of "Kharif" (monsoon) rice production, current farm income, and investment for the next crop cycle to determine the pathways and degree of the dual impact on farm households. Current household expenditure, livestock, and soil fertility were other central elements in the shared mental model. Scenario analysis with multiple stakeholders suggested enhanced market access and current household income, sustained investment in farming, rapid improvement in affected soil, irrigation water and livestock as the most effective strategies to enhance the resilience of farm families during and after the pandemic. This study may help in formulating short and long-term intervention strategies in the post-pandemic communities, and the methodological approach can be used elsewhere to understand perturbed socioecological systems to formulate anticipatory intervention strategies based on collective wisdom of stakeholders.

Machine learning identifies "rsfMRI epilepsy networks" in temporal lobe epilepsy.

OBJECTIVES: Experimental models have provided compelling evidence for the existence of neural networks in temporal lobe epilepsy (TLE). To identify and validate the possible existence of resting-state "epilepsy networks," we used machine learning methods on resting-state functional magnetic resonance imaging (rsfMRI) data from 42 individuals with TLE. METHODS: Probabilistic independent component analysis (PICA) was applied to rsfMRI data from 132 subjects (42 TLE patients + 90 healthy controls) and 88 independent components (ICs) were obtained following standard procedures. Elastic net-selected features were used as inputs to support vector machine (SVM). The strengths of the top 10 networks were correlated with clinical features to obtain "rsfMRI epilepsy networks." RESULTS: SVM could classify individuals with epilepsy with 97.5% accuracy (sensitivity = 100%, specificity = 94.4%). Ten networks with the highest ranking were found in the frontal, perisylvian, cingulo-insular, posterior-quadrant, thalamic, cerebello-thalamic, and temporo-thalamic regions. The posterior-quadrant, cerebello-thalamic, thalamic, medial-visual, and perisylvian networks revealed significant correlation (r > 0.40) with age at onset of seizures, the frequency of seizures, duration of illness, and a number of anti-epileptic drugs. CONCLUSIONS: IC-derived rsfMRI networks contain epilepsy-related networks and machine learning methods are useful in identifying these networks in vivo. Increased network strength with disease progression in these "rsfMRI epilepsy networks" could reflect epileptogenesis in TLE. KEY POINTS: • ICA of resting-state fMRI carries disease-specific information about epilepsy. • Machine learning can classify these components with 97.5% accuracy. • "Subject-specific epilepsy networks" could quantify "epileptogenesis" in vivo.

Geostatistical approach for management of soil nutrients with special emphasis on different forms of potassium considering their spatial variation in intensive cropping system of West Bengal, India.

A large part of precision agriculture research in the developing countries is devoted towards precision nutrient management aspects. This has led to better economics and efficiency of nutrient use with off-farm advantages of environmental security. The keystone of precision nutrient management is analysis and interpretation of spatial variability of soils by establishing management zones. In this study, spatial variability of major soil nutrient contents was evaluated in the Ghoragacha village of North 24 Parganas district of West Bengal, India. Surface soil samples from 100 locations, covering different cropping systems of the village, was collected from 0 to 15 cm depth using 100×100 m grid system and analyzed in the laboratory to determine organic carbon (OC), available nitrogen (N), phosphorus (P), and potassium (K) contents of the soil as well as its water-soluble K (KWS), exchangeable K (KEX), and non-exchangeable forms of K (KNEX). Geostatistical analyses were performed to determine the spatial variation structure of each nutrient content within the village, followed by the generation of surface maps through kriging. Four commonly used semivariogram models, i.e., spherical, exponential, Gaussian, and linear models were fitted to each soil property, and the best one was used to prepare surface maps through krigging. Spherical model was found the best for available N and P contents, while linear and exponential model was the best for OC and available K, and for KWS and KNEK, Gausian model was the best. Surface maps of nutrient contents showed that N content (129-195 kg ha(-1)) was the most limiting factor throughout the village, while P status was generally very high ( 10-678 kg ha(-1)) in the soils of the present village. Among the different soil K fractions, KWS registered the maximum variability (CV 75%), while the remaining soil K fractions showed moderate to high variation. Interestingly, KNEX content also showed high variability, which essentially indicates reserve native K exploitation under intensive cultivation. These maps highlight the necessity of estimating the other soil K fractions as well for better understanding of soil K supplying capacity and K fertilization strategy rather than the current recommendations, based on the plant-available K alone. In conclusion, the present study revealed that the variability of nutrient distribution was a consequence of complex interactions between the cropping system, nutrient application rates, and the native soil characteristics, and such interactions could be utilized to develop the nutrient management strategies for intensive small-holder system.

Synchronization implies seizure or seizure implies synchronization?

Epileptic seizures are considered as abnormally hypersynchronous neuronal activities of the brain. The question is "Do hypersynchronous neuronal activities in a brain region lead to seizure or the hypersynchronous activities take place due to the progression of the seizure?" We have examined the ECoG signals of 21 epileptic patients consisting of 87 focal-onset seizures by three different measures namely, phase synchronization, amplitude correlation and simultaneous occurrence of peaks and troughs. Each of the measures indicates that for a majority of the focal-onset seizures, synchronization or correlation or simultaneity occurs towards the end of the seizure or even after the offset rather than at the onset or in the beginning or during the progression of the seizure. We have also briefly discussed about a couple of synchronization dependent seizure termination mechanisms. Our conclusion is synchronization is an effect rather than the cause of a significant number of pharmacologically intractable focal-onset seizures. Since all the seizures that we have tested belong to the pharmacologically intractable class, their termination through more coherent neuronal activities may lead to new and effective ways of discovery and testing of drugs.

Co-occurrence of cytomegalovirus-induced vanishing bile duct syndrome with papillary stenosis in HIV infection.

Jaundice in patients with AIDS can be a result of diverse conditions ranging from opportunistic infections to drug-related hepatotoxicity. With the advent of antiretroviral therapy (ART), the prevalence of AIDS cholangiopathy as a cause of jaundice has decreased; on the other hand, ART-related hepatotoxicity has become one of the commonest causes of jaundice in these patients. AIDS cholangiopathy is a rare condition of extrahepatic biliary obstruction in patients with advanced HIV infection, usually due to opportunistic infections. Vanishing bile duct syndrome (VBDS) is an acquired disorder characterized by progressive destruction and loss of interlobular bile ducts causing intrahepatic cholestasis. Herein, we report co-occurrence of fatal cytomegalovirus (CMV)-induced VBDS along with papillary stenosis, as a component of AIDS cholangiopathy, which to the best of our knowledge has not been documented earlier. This is perhaps the third case of VBDS in a patient with AIDS, and the second in association with CMV infection. VBDS in AIDS has a poor outcome, and liver transplantation may be considered only in a suitable candidate.

Sphenoid wing lymphoplasmacyte-rich meningioma with occasional emperipolesis closely simulating an intracranial Rosai-Dorfman disease: a diagnostic dilemma.

In lymphoplasmacyte-rich meningioma (LRM) meningothelial whorls are overshadowed by exuberant infiltration by lymphocytes, plasma cells and few histiocytes. Hence, lesions with lymphoplasmacytic proliferation form the histological differentials. We describe the, to the best of our knowledge, first case of LRM with occasiona emperipolesis, creating a diagnostic dilemma with Rosai-Dorfman disease (RDD), around the region of sphenoid wing. LRM was favored due to the presence of epithelial membrane antigen (EMA) and vimentin positive meningothelial whorls, forming approximately 10% of the tumor tissue. Documentation of such cases may help to understand the importance of inflammatory cells and meningothelial whorls, as a manifestation of host response at the leptomeninges.

Embryonal tumor with abundant neuropil and true rosettes with melanotic (retinal) differentiation.

Embryonal tumor with abundant neuropil and true rosettes (ETANTR) is a rare variant of central nervous system primitive neuroectodermal tumor occurring exclusively in the pediatric population. We report a unique case of a 6-month male child presenting with a large intraventricular lesion. Histological examination revealed a tumor composed of primitive neuroectodermal cells in dense aggregates, interspersed by hypocellular areas containing small round cells widely dispersed in neuropil-like material. Few ependymal and occasional ependymoblastic rosettes were appreciated. Focal melanotic neuroepithelium recapitulating retinal differentiation was also seen. Documentation of such cases may expand the neuroectodermal differentiation spectrum of ETANTR.

Non-Association of Driver Alterations in PTEN with Differential Gene Expression and Gene Methylation in IDH1 Wildtype Glioblastomas.

During oncogenesis, alterations in driver genes called driver alterations (DAs) modulate the transcriptome, methylome and proteome through oncogenic signaling pathways. These modulatory effects of any DA may be analyzed by examining differentially expressed mRNAs (DEMs), differentially methylated genes (DMGs) and differentially expressed proteins (DEPs) between tumor samples with and without that DA. We aimed to analyze these modulations with 12 common driver genes in Isocitrate Dehydrogenase 1 wildtype glioblastomas (IDH1-W-GBs). Using Cbioportal, groups of tumor samples with and without DAs in these 12 genes were generated from the IDH1-W-GBs available from "The Cancer Genomics Atlas Firehose Legacy Study Group" (TCGA-FL-SG) on Glioblastomas (GBs). For all 12 genes, samples with and without DAs were compared for DEMs, DMGs and DEPs. We found that DAs in PTEN were unassociated with any DEM or DMG in contrast to DAs in all other drivers, which were associated with several DEMs and DMGs. This contrasting PTEN-related property of being unassociated with differential gene expression or methylation in IDH1-W-GBs was unaffected by concurrent DAs in other common drivers or by the types of DAs affecting PTEN. From the lists of DEMs and DMGs associated with some common drivers other than PTEN, enriched gene ontology terms and insights into the co-regulatory effects of these drivers on the transcriptome were obtained. The findings from this study can improve our understanding of the molecular mechanisms underlying gliomagenesis with potential therapeutic benefits.

A mathematical model for astrocytes mediated LTP at single hippocampal synapses.

Many contemporary studies have shown that astrocytes play a significant role in modulating both short and long form of synaptic plasticity. There are very few experimental models which elucidate the role of astrocyte over Long-term Potentiation (LTP). Recently, Perea and Araque (Science 317:1083-1086, 2007) demonstrated a role of astrocytes in induction of LTP at single hippocampal synapses. They suggested a purely pre-synaptic basis for induction of this N-methyl-D-Aspartate (NMDA) Receptor-independent LTP. Also, the mechanisms underlying this pre-synaptic induction were not investigated. Here, in this article, we propose a mathematical model for astrocyte modulated LTP which successfully imitates the experimental findings of Perea and Araque (Science 317:1083-1086, 2007). Our study suggests the role of retrograde messengers, possibly Nitric Oxide (NO), for this pre-synaptically modulated LTP.

Multicentric extranodal Rosai Dorfman disease--a cytological diagnosis, with histological corroboration.

BACKGROUND: Rosai Dorfman disease (RDD) typically presents with massive bilateral cervical lymphadenopathy, a viral-like prodrome, elevated erythrocyte sedimentation rate, and polyclonal hypergammaglobulinemia. Other lymph nodes may be less commonly involved. Extranodal RDD is quite rare, and orbital disease accounts for only 10% of the extranodal sites of involvement. Multicentric disease has also been described, which is usually accompanied by lymphadenopathy either initially or later in the disease course. CASE: We report an extremely rare extranodal multicentric disease in a diabetic patient, presenting with bilateral orbital involvement, causing ocular motility restriction, which was diagnosed on aspiration cytology of the orbital mass. This was followed in quick succession by new mass lesions in the lower back and infratemporal fossa. On extensive work-up, no lymphadenopathy was detected. The patient responded well to surgical debulking of the orbital lesions and systemic steroids. CONCLUSION: Fine needle aspiration cytology can be effectively applied for early diagnosis of multicentric extranodal RDD. Surgical debulking in such cases may be supplemented by systemic steroids.

A mathematical model of the tripartite synapse: astrocyte-induced synaptic plasticity.

In this paper, we present a biologically detailed mathematical model of tripartite synapses, where astrocytes modulate short-term synaptic plasticity. The model consists of a pre-synaptic bouton, a post-synaptic dendritic spine-head, a synaptic cleft and a peri-synaptic astrocyte controlling Ca(2 + ) dynamics inside the synaptic bouton. This in turn controls glutamate release dynamics in the cleft. As a consequence of this, glutamate concentration in the cleft has been modeled, in which glutamate reuptake by astrocytes has also been incorporated. Finally, dendritic spine-head dynamics has been modeled. As an application, this model clearly shows synaptic potentiation in the hippocampal region, i.e., astrocyte Ca(2 + ) mediates synaptic plasticity, which is in conformity with the majority of the recent findings (Perea and Araque (Science 317, 1083-1086, 2007); Henneberger et al. (Nature 463, 232-236, 2010); Navarrete et al. (PLoS Biol. 10, e1001259, 2012)).

Pediatric hydronephrotic segmental renal dysplasia with ipsilateral ureterovesical obstruction--rare coincidence or a consequence?

Obstruction in the developing urinary tract during embryonic life is one of the factors promoting disordered metanephric development in renal dysplasia. Dysplastic kidneys usually undergo involution during the first 5 years of life. Herein, we narrate a rare case of hydronephrotic segmental dysplasia co-existing with ipsilateral ureterovesical obstruction, in a 7-year-old male child, masquerading as hydronephrosis. Etiopathogenesis of segmental dysplasia presenting at this age is not clearly understood, and could be a consequence of intrauterine obstructive uropathy. Histologic evidence of dysplasia in a hydronephrotic kidney should warrant a close follow-up for pathologic changes in the contralateral kidney or urinary tract.

Alveolar soft part sarcoma of the retroperitoneum: A case report.

Alveolar soft part sarcoma is a rare soft tissue tumor with uncertain histogenesis. It is a slow growing tumor with a high rate of metastasis. The tumor is not easily identified as clinical symptoms are not pronounced. The retroperitoneum is a rare location of tumor, with a few cases published in literature. Surgical excision is the mainstay of treatment. Here we describe a rare case of a large retroperitoneal Alveolar soft part sarcoma in a young female with radiological and histopathological findings.

Life After Death.

OBJECTIVES: To test the performance characteristics of 69 primary immunohistochemistry antibodies after expiration and compare with fresh primary antibodies wherever possible. METHODS: A total of 69 expired primary antibodies were evaluated for specificity, background staining, and intensity. An optimal staining result corresponded to a semiquantitatively scored 2+ or 3+ intensity, with intact specificity devoid of moderate or strong background staining. Any deviation from a normal staining pattern was also considered to be a suboptimal result. RESULTS: Nearly half of the antibodies studied showed an optimally positive staining result after expiration (34/69, 49.2%). Overall, 10.1% (7/69) of antibodies could be compared with fresh primary antibodies of the same clone with equivalent results. Eight of 69 (11.6%) expired antibodies showed splotchy or granular staining. CONCLUSIONS: Evidence from this study and previous work point to maintained functionality of a fair number of primary immunohistochemical antibodies after expiration. Decisions about the use of such reagents should be guided by a thorough assessment of functionality by the pathologist rather than a manufacturer-specified deadline. Quality maintenance should imply a sensible balance between histopathologic performance and economics.

Crop nutrient management using Nutrient Expert improves yield, increases farmers' income and reduces greenhouse gas emissions.

Reduction of excess nutrient application and balanced fertilizer use are the key mitigation options in agriculture. We evaluated Nutrient Expert (NE) tool-based site-specific nutrient management (SSNM) in rice and wheat crops by establishing 1594 side-by-side comparison trials with farmers' fertilization practices (FFP) across the Indo-Gangetic Plains (IGP) of India. We found that NE-based fertilizer management can lower global warming potential (GWP) by about 2.5% in rice, and between 12 and 20% in wheat over FFP. More than 80% of the participating farmers increased their crop yield and farm income by applying the NE-based fertilizer recommendation. We also observed that increased crop yield and reduced fertilizer consumption and associated greenhouse gas (GHG) emissions by using NE was significantly influenced by the crop type, agro-ecology, soil properties and farmers' current level of fertilization. Adoption of NE-based fertilizer recommendation practice in all rice and wheat acreage in India would translate into 13.92 million tonnes (Mt) more rice and wheat production with 1.44 Mt less N fertilizer use, and a reduction in GHG of 5.34 Mt CO2e per year over farmers' current practice. Our study establishes the utility of NE to help implement SSNM in smallholder production systems for increasing crop yields and farmers' income while reducing GHG emissions.

Enhanced gamma band mutual information is associated with impaired consciousness during temporal lobe seizures.

BACKGROUND: Epileptic seizures are characterized by aberrant synchronization. We hypothesized that higher synchronization across the seizure onset zone (SOZ) channels during a temporal lobe seizure contributes to impaired consciousness. NEW METHOD: All symmetric bivariate synchronization measures were extended to multivariate measure by a principal component analysis (PCA) based technique. A novel nonparametric method has been proposed to test the statistical significance between increased synchronization across the seizure onset zone (SOZ) channels and reduced consciousness. RESULTS: Increased synchronization in the gamma band towards seizure termination significantly contributes to impaired consciousness (p < 0.1). Synchronization reaches its peak in the extratemporal region (frontal lobe) ahead of the temporal region (p < 0.05). Synchronization is prominent in beta and gamma bands by most methods and it is more in the second half of seizure duration than in the first (p < 0.05). CONCLUSIONS: Mutual information is the only synchronization measure out of the six that we studied, whose increase can be associated with the loss of consciousness in a statistically significant way.

HER-2/neu over expression in gall bladder adenocarcinoma: A quest for potential therapeutic target.

BACKGROUND: Gall bladder carcinoma (GBC) is an aggressive malignancy with high mortality and aggressive course, with palliation as the only available option. OBJECTIVES: To evaluate frequency of HER-2/neu overexpression in GBC and to seek its correlation, if any with conventional clinicopathological parameters and survival. METHODS: Immunohistochemistry (IHC) was performed on 200 cases of GBC, 32 cases of dysplasia, and 100 cases of chronic cholecystitis. Fluorescent in situ hybridization (FISH) was performed on 30 randomly selected cases of GBC to validate IHC. HER-2/neu overexpression (IHC 3+/FISH amplification ≥2.2) was correlated with clinicopathological parameters by Chi-square test.P < 0.05 was considered significant. Survival analysis was done by log-rank test and Kaplan-Meier analysis. RESULTS: HER-2/neu overexpression was seen in 14% (28/200) GBC cases but was not found in dysplasia and chronic cholecystitis. Majority of these cases were ≤grade 2 and in advanced stage, however this was not statistically significant. A lower mean survival in HER-2/neu positive group as compared to HER-2/neu negative group (17.1 ± 2.3 month versus 67.6 ± 8.5 month, respectively) was observed. Concordance between IHC and FISH was seen in 18/19 cases. CONCLUSION: This study delineates a subset of GBC patients with HER-2/neu overexpression, in whom targeted therapy can offer a survival benefit.