Exact genome alignment

The increase in the volume of genomic data due to the decrease in the cost of whole genome sequencing techniques has opened up new avenues of research in the field of Bioinformatics, like comparative genomics and evolutionary dynamics. The fundamental task in these studies is to align the genome sequences accurately. Sequence alignment helps to identify regions of similarity between the sequences to establish their functional, evolutionary and structural relationship. The thesis investigates the performance of two sequence alignment programs LASTZ, a hash table based faster method and SSEARCH, a slower but more rigorous Smith-Waterman based approach, on whole genome sequences from primates and mammals. An exact genome alignment technique is used by breaking the entire genome into fragments and aligning these fragments with the reference genome using the Smith-Waterman based method. A comparison of the two methods reveals that the second approach performs better for genomes from closely related species

Too Much or Too Little? Paradoxes of Disability and Care Work in India

The notion of care often normalizes within it violence that can have devastating effects on the lives of disabled people. Cripping care critiques the normalization of such notions of care. This paper articulates this paradox of care within the lived experiences of disabled girls and their mothers as primary carers. Through extensive case studies of young, disabled girls and their carers in villages of West Bengal, Jharkhand, and Odisha in India—where abject poverty, lack of resources, and a dearth of sensitized social relationships remain entrenched—this paper problematizes care relationships, moving beyond social model approaches to include understandings from the Global South of what it might mean to crip care. The paper explores care relationships within the family, which valorize the emotional and physical labor of women in the garb of motherhood while negating the personhood of disabled daughters. While the care relationship between mother and daughter is enhanced by the affective bonds of empathy, emotional responsiveness, and perceptual attentiveness that transform intimate tasks into relationships of trust and demonstrations of trustworthiness, in the unforgiving realities of rural poverty in India the collective act of survival of such families needs to be contextualized within the debates about cripping care

Citizenship, Rights and Persons with Disabilities in India

The neo-liberal discourse of rights focuses on rights-based legislations and empowers citizens to place claims on the state. The push toward a rights-based approach in India by disability activists sought to shift the underlying power dynamic between citizens and the state through legislation. However, such rights-based discourses underplay or negate intra-group power politics that influence claims to rights and entitlements. This paper attempts to explore the ways in which disability groups in India engaged with the concept of citizenship in the debates prior to the passage of the Rights of Persons with Disabilities Act 2016. As citizenship creates whole categories of people who are subject to the government’s authority, an attempt will be made to see how actors within the rights movements interacted among themselves and with the state, to ensure welfare provisions as well as citizenship rights for different groups of people from different impairment categories

Introduction. Debating Intersectionalities: Challenges for a Methodological Framework

Intersectionality is primarily an organizing principle which calls for reflexivity in the study of social characteristics, such that one marginality is not substituted for another and lived experiences are not treated as generic and undifferentiated. Critiques of intersectionality have feared that intersectionality results in the fragmentation of the opposition to structural oppression. We argue for the potentialities of a reflexive use of intersectionality rather than its rejection, for this intersectionality has to be applied as a method of research. Lived experiences provide the possibility to explore how intersectionality works in practice. By mapping the fractured nature of the everyday, a lived-experience approach allows us to be open to competing interpretations, thereby not only illustrating the multi-dimensionality of what is constructed as hegemonic fact, but also can in fact script some resistance to it. Consequently, this article thus argues in addition in favor of a radical intersectional praxis as a means of building coalitions across marginalities

Data on mass spectrometry based identification of allergens from sunflower (Helianthus annuus L.) pollen proteome

AbstractAllergy is a type of abnormal immune reactions, which is triggered by environmental antigens or allergens and mediated by IgE antibodies. Now-a-days mass spectrometry is the method of choice for allergen identification based on homology searching. Here, we provide the mass spectrometry dataset associated with our previously published research article on identification of sunflower pollen allergens (Ghosh et al., 2015 [1]). In this study allergenicity of sunflower (Helianthus annuus) pollen grains were primarily investigated by clinical studies followed by detailed immunobiochemical and immunoproteomic analyses. The mass spectrometry data for the identification of allergens were deposited to ProteomeXchange Consortium via PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD002397

Abnormalities in semen analysis among male partners of infertile couples: a study in a tertiary care level hospital of West Bengal, India

Background: The prevalence of infertility in the general population is 15%-20%. Of this, the male factor is responsible for 20%-40%.Analysis of semen is the most important diagnostic tool for evaluation of role of males in infertility. The study was conducted to determine the abnormalities in semen among male partners in infertile couples.Methods: A descriptive study with cross-sectional design among male partners of infertile couples was conducted in the laboratory of the Department of Pathology at Burdwan Medical College, Burdwan in West Bengal during August 2011 to July 2012. Analysis of semen was done for semen volume, sperm number, sperm motility and presence of other cells.Results: 7.45% samples were of inadequate quantity. 19.87 % of cases had oligozoospermia, 12.42% had azoospermia and 4.35% of males had asthenozoospermia. Pus cells were found in 12.42% cases.Conclusions: Majority of the cases of infertility in males is due to oligozoospermia followed by azoospermia while less sperm motility or less amount of semen are also responsible in some cases

A Modified Collagen Dressing Induces Transition of Inflammatory to Reparative Phenotype of Wound Macrophages

Collagen containing wound-care dressings are extensively used. However, the mechanism of action of these dressings remain unclear. Earlier studies utilizing a modified collagen gel (MCG) dressing demonstrated improved vascularization of ischemic wounds and better healing outcomes. Wound macrophages are pivotal in facilitating wound angiogenesis and timely healing. The current study was designed to investigate the effect of MCG on wound macrophage phenotype and function. MCG augmented recruitment of macrophage at the wound-site, attenuated pro-inflammatory and promoted anti-inflammatory macrophage polarization. Additionally, MCG increased anti-inflammatory IL-10, IL-4 and pro-angiogenic VEGF production, indicating a direct role of MCG in resolving wound inflammation and improving angiogenesis. At the wound-site, impairment in clearance of apoptotic cell bioburden enables chronic inflammation. Engulfment of apoptotic cells by macrophages (efferocytosis) resolves inflammation via a miR-21-PDCD4-IL-10 pathway. MCG-treated wound macrophages exhibited a significantly bolstered efferocytosis index. Such favorable outcome significantly induced miR-21 expression. MCG-mediated IL-10 production was dampened under conditions of miR-21 knockdown pointing towards miR-21 as a causative factor. Pharmacological inhibition of JNK attenuated IL-10 production by MCG, implicating miR-21-JNK pathway in MCG-mediated IL-10 production by macrophages. This work provides direct evidence demonstrating that a collagen-based wound-care dressing may influence wound macrophage function and therefore modify wound inflammation outcomes

Evidence of enhanced thermopower from emergent local moments in flatbands of magic-angle twisted bilayer graphene

Recent experiments on magic-angle twisted bilayer graphene (MATBLG) indicate an unusual coexistence of heavy and light electrons, characteristic of Heavy-Fermion physics. Yet, these experiments lack direct evidence of the existence of local moments associated with the heavy electrons, a key component of Heavy-Fermion physics. Thermopower serves as a sensitive probe for measuring entropy and can, therefore, unveil the presence of local moments by assessing their impact on entropy. In this work, we have carried out comprehensive thermopower studies on MATBLG by varying temperatures ($T$) and magnetic fields ($B$). While the resistance exhibits prominent resistance peaks at integer fillings apart from the Dirac point (DP, $\nu = 0$) and full band filling ($\nu = \pm 4$), the thermopower remains featureless and symmetric to the DP with opposite signs, in complete violation of the Mott formula, even up to $\sim 100K$. This discrepancy indicates that resistance and thermopower are carried by different kinds of carriers. With the expected sign changes at the DP and full band filling, the thermopower demonstrates additional sign changes within the conduction and valence bands around $\nu \sim \pm 1$, persisting from $5K$ to $50K$. These observations cannot be explained solely by thermopower arising from an emergent Heavy-Fermion band picture, which is highly sensitive to temperature. Instead, our data is consistent with the dominant contribution coming from the entropy of the localized moments of heavy electrons. To validate the claim, we studied the thermopower with $B_{\parallel}$ and $B_{\perp}$, revealing a $30\%$ and $50\%$ reduction, respectively, and attributed to the partial polarization of the local moments (spin/valley), resulting in decreased entropy. Our results highlight the thermopower contribution from local moments and establish the Heavy-Fermion physics in MATBLG

Outcomes of treatment of unresectable esophageal carcinoma treated with chemoradiotherapy and oral metronomic chemotherapy: An experience from a rural cancer center

Introduction: Esophageal carcinoma is the eight most common cancer in the world. The management of locally advancedcarcinoma esophagus is mainly palliative with chemoradiotherapy. The outcome data of such a modality along with oralmetronomic chemotherapy after treatment completion are sparse. Here, we present the outcomes of treatment of locally advancedunresectable esophageal cancer after palliative chemoradiotherapy and oral metronomic therapy from a rural setting in India.Methods: Retrospective analysis of all patients of locally advanced unresectable nonmetastatic esophageal carcinoma treatedwith short course of induction chemotherapy followed by radiotherapy/chemoradiotherapy and oral metronomic chemotherapywas performed. The primary aim was estimation of progression free-survival (PFS) and overall survival (OS). Results: A total of45 patients were analyzed. Mean age was 55 years (30-85 years). A total of 32 patients had tumors in upper and middle esophagus,with the most common histology being squamous cell carcinoma (N-41). The estimated 2 year PFS is 47.2% and the estimated2 years OS is 57.8%. Conclusion: Combined modality therapy with adjuvant oral metronomic therapy shows promising results inthe management and should be the basis of further trials