CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution

MOTIVATION

Complex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments.

RESULTS

We previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable.

AVAILABILITY AND IMPLEMENTATION

The open-source R Scripts of CAM3.0 is freely available at https://github.com/ChiungTingWu/CAM3/(https://github.com/Bioconductor/Contributions/issues/3205). A user's guide and a vignette are provided.

Exploring the role of electrostatic deposition on inhaled aerosols in alveolated microchannels

Large amounts of net electrical charge are known to accumulate on inhaled aerosols during their generation using commonly-available inhalers. This effect often leads to superfluous deposition in the extra-thoracic airways at the cost of more efficient inhalation therapy. Since the electrostatic force is inversely proportional to the square of the distance between an aerosol and the airway wall, its role has long been recognized as potentially significant in the deep lungs. Yet, with the complexity of exploring such phenomenon directly at the acinar scales, in vitro experiments have been largely limited to upper airways models. Here, we devise a microfluidic alveolated airway channel coated with conductive material to quantify in vitro the significance of electrostatic effects on inhaled aerosol deposition. Specifically, our aerosol exposure assays showcase inhaled spherical particles of 0.2, 0.5, and 1.1 μm that are recognized to reach the acinar regions, whereby deposition is typically attributed to the leading roles of diffusion and sedimentation. In our experiments, electrostatic effects are observed to largely prevent aerosols from depositing inside alveolar cavities. Rather, deposition is overwhelmingly biased along the inter-alveolar septal spaces, even when aerosols are charged with only a few elementary charges. Our observations give new insight into the role of electrostatics at the acinar scales and emphasize how charged particles under 2 µm may rapidly overshadow the traditionally accepted dominance of diffusion or sedimentation when considering aerosol deposition phenomena in the deep lungs.

ABDS: tool suite for analyzing biologically diverse samples

Motivation

Analytics tools are essential to identify informative molecular features about different phenotypic groups. Among the most fundamental tasks are missing value imputation, signature gene detection, and expression pattern visualization. However, most commonly used analytics tools may be problematic for characterizing biologically diverse samples when either signature genes possess uneven missing rates across different groups yet involving complex missing mechanisms, or multiple biological groups are simultaneously compared and visualized.

Results

We develop ABDS tool suite tailored specifically to analyzing biologically diverse samples. Mechanism-integrated group-wise imputation is developed to recruit signature genes involving informative missingness, cosine-based one-sample test is extended to detect enumerated signature genes, and unified heatmap is designed to comparably display complex expression patterns. We discuss the methodological principles and demonstrate the conceptual advantages of the three software tools. We also showcase the biomedical applications of these individual tools. Implemented in open-source R scripts, ABDS tool suite complements rather than replaces the existing tools and will allow biologists to more accurately detect interpretable molecular signals among diverse phenotypic samples.

Availability and implementation

The R Scripts of ABDS tool suite is freely available at https://github.com/niccolodpdu/ABDS.

In vitro-in silico correlation of three-dimensional turbulent flows in an idealized mouth-throat model

There exists an ongoing need to improve the validity and accuracy of computational fluid dynamics (CFD) simulations of turbulent airflows in the extra-thoracic and upper airways. Yet, a knowledge gap remains in providing experimentally-resolved 3D flow benchmarks with sufficient data density and completeness for useful comparison with widely-employed numerical schemes. Motivated by such shortcomings, the present work details to the best of our knowledge the first attempt to deliver in vitro-in silico correlations of 3D respiratory airflows in a generalized mouth-throat model and thereby assess the performance of Large Eddy Simulations (LES) and Reynolds-Averaged Numerical Simulations (RANS). Numerical predictions are compared against 3D volumetric flow measurements using Tomographic Particle Image Velocimetry (TPIV) at three steady inhalation flowrates varying from shallow to deep inhalation conditions. We find that a RANS k-ω SST model adequately predicts velocity flow patterns for Reynolds numbers spanning 1'500 to 7'000, supporting results in close proximity to a more computationally-expensive LES model. Yet, RANS significantly underestimates turbulent kinetic energy (TKE), thus underlining the advantages of LES as a higher-order turbulence modeling scheme. In an effort to bridge future endevours across respiratory research disciplines, we provide end users with the present in vitro-in silico correlation data for improved predictive CFD models towards inhalation therapy and therapeutic or toxic dosimetry endpoints.

Information set supported deep learning architectures for improving noisy image classification

Deep learning models have been widely used in many supervised learning applications. However, these models suffer from overfitting due to various types of uncertainty with deteriorating performance when facing data biases, class imbalance, or noise propagation. The Information-Set Deep learning (ISDL) architectures with four variants are developed by integrating information set theory and deep learning principles to address the critical problem of the absence of robust deep learning models. There is a description of the ISDL architectures, learning algorithms, and analytic workflows. The performance of the ISDL models and standard architectures is evaluated using a noise-corrupted benchmark dataset. The experimental results show that the ISDL models can efficiently handle noise-dominated uncertainty and outperform peer architectures.

A Novel Trans-Tracheostomal Retrograde Inhalation Technique Increases Subglottic Drug Deposition Compared to Traditional Trans-Oral Inhalation

Subglottic stenosis represents a challenging clinical condition in otolaryngology. Although patients often experience improvement following endoscopic surgery, recurrence rates remain high. Pursuing measures to maintain surgical results and prevent recurrence is thus necessary. Steroids therapy is considered effective in preventing restenosis. Currently, however, the ability of trans-oral steroid inhalation to reach and affect the stenotic subglottic area in a tracheotomized patient is largely negligible. In the present study, we describe a novel trans-tracheostomal retrograde inhalation technique to increase corticosteroid deposition in the subglottic area. We detail our preliminary clinical outcomes in four patients treated with trans-tracheostomal corticosteroid inhalation via a metered dose inhaler (MDI) following surgery. Concurrently, we leverage computational fluid-particle dynamics (CFPD) simulations in an extra-thoracic 3D airway model to gain insight on possible advantages of such a technique over traditional trans-oral inhalation in augmenting aerosol deposition in the stenotic subglottic region. Our numerical simulations show that for an arbitrary inhaled dose (aerosols spanning 1–12 µm), the deposition (mass) fraction in the subglottis is over 30 times higher in the retrograde trans-tracheostomal technique compared to the trans-oral inhalation technique (3.63% vs. 0.11%). Importantly, while a major portion of inhaled aerosols (66.43%) in the trans-oral inhalation maneuver are transported distally past the trachea, the vast majority of aerosols (85.10%) exit through the mouth during trans-tracheostomal inhalation, thereby avoiding undesired deposition in the broader lungs. Overall, the proposed trans-tracheostomal retrograde inhalation technique increases aerosol deposition rates in the subglottis with minor lower-airway deposition compared to the trans-oral inhalation technique. This novel technique could play an important role in preventing restenosis of the subglottis.

Modeling Flow in an In Vitro Anatomical Cerebrovascular Model with Experimental Validation

Acute ischemic stroke (AIS) is a leading cause of mortality that occurs when an embolus becomes lodged in the cerebral vasculature and obstructs blood flow in the brain. The severity of AIS is determined by the location and how extensively emboli become lodged, which are dictated in large part by the cerebral flow and the dynamics of embolus migration which are difficult to measure in vivo in AIS patients. Computational fluid dynamics (CFD) can be used to predict the patient-specific hemodynamics and embolus migration and lodging in the cerebral vasculature to better understand the underlying mechanics of AIS. To be relied upon, however, the computational simulations must be verified and validated. In this study, a realistic in vitro experimental model and a corresponding computational model of the cerebral vasculature are established that can be used to investigate flow and embolus migration and lodging in the brain. First, the in vitro anatomical model is described, including how the flow distribution in the model is tuned to match physiological measurements from the literature. Measurements of pressure and flow rate for both normal and stroke conditions were acquired and corresponding CFD simulations were performed and compared with the experiments to validate the flow predictions. Overall, the CFD simulations were in relatively close agreement with the experiments, to within ±7% of the mean experimental data with many of the CFD predictions within the uncertainty of the experimental measurement. This work provides an in vitro benchmark data set for flow in a realistic cerebrovascular model and is a first step towards validating a computational model of AIS.

Modeling flow in an in vitro anatomical cerebrovascular model with experimental validation

Acute ischemic stroke (AIS) is a leading cause of mortality that occurs when an embolus becomes lodged in the cerebral vasculature and obstructs blood flow in the brain. The severity of AIS is determined by the location and how extensively emboli become lodged, which are dictated in large part by the cerebral flow and the dynamics of embolus migration which are difficult to measure in vivo in AIS patients. Computational fluid dynamics (CFD) can be used to predict the patient-specific hemodynamics and embolus migration and lodging in the cerebral vasculature to better understand the underlying mechanics of AIS. To be relied upon, however, the computational simulations must be verified and validated. In this study, a realistic in vitro experimental model and a corresponding computational model of the cerebral vasculature are established that can be used to investigate flow and embolus migration and lodging in the brain. First, the in vitro anatomical model is described, including how the flow distribution in the model is tuned to match physiological measurements from the literature. Measurements of pressure and flow rate for both normal and stroke conditions were acquired and corresponding CFD simulations were performed and compared with the experiments to validate the flow predictions. Overall, the CFD simulations were in relatively close agreement with the experiments, to within ±7% of the mean experimental data with many of the CFD predictions within the uncertainty of the experimental measurement. This work provides an in vitro benchmark data set for flow in a realistic cerebrovascular model and is a first step towards validating a computational model of AIS.

Organizations Take Initiatives For The Development Of Women Leaders

Purpose: 1) To Understand the male to female ratio prevailing in the organization 2) To Understand how effective are women development initiatives in organizations from a women’s perspective to determine if they will be appreciated and perceived as positive by the women. 3) To understand if the presence of women leaders in the organization leads to better engagement. 4) To understand, as suggested by research, are women leaders warmer and more male leaders more aggressive? Research Methodology: Sample - The sample size would be 50 men and women from all over India belonging to different age groups between 25-50 and are currently working in various corporations • Primary Research: In-Depth Interview, Survey • Secondary research: literature review • Analysis of the collected data Practical Implications: This will help identify why, even though there is awareness about the importance of having women leaders, the initiatives were taken for their development have not contributed significantly. This paper will help understand if these initiatives are enough in the given culture of the organization that has pre-defined norms and expectations from a woman’s standpoint of view. Originality: This research will mainly focus on the view of women about development initiatives in the organization.

Deceased Donor Renal Transplantation: 6 Year Experience from a Tertiary Care Center in North India

The incident of End stage renal disease (ESRD) is rising rapidly worldwide. Renal transplant is the best modality of treatment, offering a better quality of life and mortality benefit, as compared with long-term dialysis. Very few patients have a live renal transplant donor, for rest, a decreased donor renal transplant is the only alternative. Deceased donor renal transplantation (DDRT) programs are only available at few government centers of India, constituting less than 5% of the total renal transplants.

MATERIAL

The patients who had undergone DDRT at our center from February 2015 to February 2021 were registered in the study. The following data were recorded for all patients; age, sex, duration of ESRD, cold ischemia time, type of induction, nadir and follow -up creatinine, hemoglobin, urinary protein and complications. All recipients were followed up and investigated in the outpatient department on a regular basis as per the standard guidelines till death or graft loss, whichever is earlier. Post transplant renal allograft function was measured using serum creatinine and other parameters.

OBSERVATION

During the study period 51 DDRTs were done. There were 40 male and 11 female patients. The mean age was 39.9 ± 9.8 years. The most common cause of ESRD in recipients was chronic glomerulonephritis (CGN) in 92.1 % (47). Amongst the patients, 41 (80.3%) survived, while 10 (19.6%) died post-transplant. Out of ten, 6 recipients died due to early sepsis (<3 months) and 4 died due to late sepsis (>3 months). Acute rejection was present in 17.6 % of patients. Mean post- transplant creatinine in recipients with functioning graft at discharge was 1.54 mg/dl. Graft failure was present in 7 patients out of which 2 were alive at the time of writing this paper and were on maintenance dialysis. Two patients died with a functioning graft. Delayed graft function (DGF) was seen in 13.7% (n=7) of recipients. The causes of DGF in our study included transplant renal artery thrombosis (n=2), Antibody-Mediated Rejection (n=3), mixed rejection (n=1) and Acute cellular rejection (n=1). Among those who had DGF, graft loss was seen in 57.2% (n=4).

CONCLUSION

In our study, the patient survival and graft survival have been better as compared to previous studies and also the number of recipients with delayed graft function have been low. Deceased donor renal transplantation is a practical treatment modality which can drastically improve longevity and quality of life.

Human Multi-Compartment Airways-on-Chip Platform for Emulating Respiratory Airborne Transmission: From Nose to Pulmonary Acini

The past decade has witnessed tremendous endeavors to deliver novel preclinical in vitro lung models for pulmonary research endpoints, including foremost with the advent of organ- and lung-on-chips. With growing interest in aerosol transmission and infection of respiratory viruses within a host, most notably the SARS-CoV-2 virus amidst the global COVID-19 pandemic, the importance of crosstalk between the different lung regions (i.e., extra-thoracic, conductive and respiratory), with distinct cellular makeups and physiology, are acknowledged to play an important role in the progression of the disease from the initial onset of infection. In the present Methods article, we designed and fabricated to the best of our knowledge the first multi-compartment human airway-on-chip platform to serve as a preclinical in vitro benchmark underlining regional lung crosstalk for viral infection pathways. Combining microfabrication and 3D printing techniques, our platform mimics key elements of the respiratory system spanning (i) nasal passages that serve as the alleged origin of infections, (ii) the mid-bronchial airway region and (iii) the deep acinar region, distinct with alveolated airways. Crosstalk between the three components was exemplified in various assays. First, viral-load (including SARS-CoV-2) injected into the apical partition of the nasal compartment was detected in distal bronchial and acinar components upon applying physiological airflow across the connected compartment models. Secondly, nebulized viral-like dsRNA, poly I:C aerosols were administered to the nasal apical compartment, transmitted to downstream compartments via respiratory airflows and leading to an elevation in inflammatory cytokine levels secreted by distinct epithelial cells in each respective compartment. Overall, our assays establish an in vitro methodology that supports the hypothesis for viral-laden airflow mediated transmission through the respiratory system cellular landscape. With a keen eye for broader end user applications, we share detailed methodologies for fabricating, assembling, calibrating, and using our multi-compartment platform, including open-source fabrication files. Our platform serves as an early proof-of-concept that can be readily designed and adapted to specific preclinical pulmonary research endpoints.

Quantitative morphology of femtosecond laser-written point-by-point optical fiber Bragg gratings

We investigate the morphology of femtosecond laser, single pulse-inscribed, point-by-point (PbP) fiber Bragg gratings. Direct measurement of a PbP grating's refractive index profile was carried out with micro-reflectivity analysis. PbP gratings were imaged at sub-micrometer scale with scanning electron microscopy, Raman and photoluminescence studies were performed to probe the structural and electronic changes. Comparison of results from different characterisation techniques suggests that the creation of an increased refractive index region around the micro-void is due to contributions from both densification and the formation of highly polarizable non-bridging oxygen bonds.

Ventilation‐induced epithelial injury drives biological onset of lung trauma in vitro and is mitigated with prophylactic anti‐inflammatory therapeutics

Mortality rates among patients suffering from acute respiratory failure remain perplexingly high despite the maintenance of blood oxygen homeostasis during ventilatory support. The biotrauma hypothesis advocates that mechanical forces from invasive ventilation trigger immunological mediators that spread systemically. Yet, how these forces elicit an immune response remains unclear. Here, a biomimetic in vitro three‐dimensional (3D) upper airways model allows to recapitulate lung injury and immune responses induced during invasive mechanical ventilation in neonates. Under such ventilatory support, flow‐induced stresses injure the bronchial epithelium of the intubated airways model and directly modulate epithelial cell inflammatory cytokine secretion associated with pulmonary injury. Fluorescence microscopy and biochemical analyses reveal site‐specific susceptibility to epithelial erosion in airways from jet‐flow impaction and are linked to increases in cell apoptosis and modulated secretions of cytokines IL‐6, ‐8, and ‐10. In an effort to mitigate the onset of biotrauma, prophylactic pharmacological treatment with Montelukast, a leukotriene receptor antagonist, reduces apoptosis and pro‐inflammatory signaling during invasive ventilation of the in vitro model. This 3D airway platform points to a previously overlooked origin of lung injury and showcases translational opportunities in preclinical pulmonary research toward protective therapies and improved protocols for patient care.

Acute coronary syndrome in young males after a prolonged stay at high altitude

The Indian population is predisposed to acute coronary syndrome at a younger age, but very few cases are reported at high altitude. Acute coronary syndrome is frequently associated with multiple cardiovascular risk factors. During management of seven young patients with acute coronary syndrome, it was found that none of them had conventional cardiovascular risk factors including recent physical exertion. It is a known fact that the risk of vascular thrombosis increases by 30 times in Indian soldiers after a long stay at high altitude. Therefore, it is necessary to carry out the tests for procoagulant markers to know whether the acute coronary syndrome was because of the prothrombotic state, and if yes, was high altitude responsible for the procoagulant state or whether the person per se had a procoagulant syndrome. With the absence of these tests at hospitals at high-altitude areas, it becomes difficult to ascertain the exact cause of acute coronary syndrome. This study highlights the importance of aggressively testing for procoagulant markers in young patients presenting with chest pain at high altitude, even in the absence of traditional risk factors.

Immunotherapy for Alzheimer's Disease: Current Scenario and Future Perspectives

Alzheimer's disease (AD) is a global health concern owing to its complexity, which often poses a great challenge to the development of therapeutic approaches. No single theory has yet accounted for the various risk factors leading to the pathological and clinical manifestations of dementia-type AD. Therefore, treatment options targeting various molecules involved in the pathogenesis of the disease have been unsuccessful. However, the exploration of various immunotherapeutic avenues revitalizes hope after decades of disappointment. The hallmark of a good immunotherapeutic candidate is not only to remove amyloid plaques but also to slow cognitive decline. In line with this, both active and passive immunotherapy have shown success and limitations. Recent approval of aducanumab for the treatment of AD demonstrates how close passive immunotherapy is to being successful. However, several major bottlenecks still need to be resolved. This review outlines recent successes and challenges in the pursuit of an AD vaccine.

Erratum: Azimuthal Anisotropy at the Relativistic Heavy Ion Collider: The First and Fourth Harmonics [Phys. Rev. Lett. 92, 062301 (2004)]

This corrects the article DOI: 10.1103/PhysRevLett.92.062301.

Treatment for kratom abuse in a contingency-management-based MAT setting: A case series

Kratom (Mitragyna speciosa) is a plant extract that exhibits opioid agonistic activity at the µ-opioid receptor. The use of this substance has increased recently due to widespread local availability across the United States, primarily at gas stations. Repeated kratom use has been shown to have major adverse effects leading to physiological dependence and addiction similar to other opioids. We used a novel contingency management (CM) program utilizing nonmonetary reinforcers along with medication-assisted treatment (MAT) using buprenorphine in an office-based setting to treat kratom use disorder in two cases. MAT with buprenorphine in a CM-based setting was found to be an effective strategy for treating kratom use disorder.

In Silico Optimization of Fiber-Shaped Aerosols in Inhalation Therapy for Augmented Targeting and Deposition across the Respiratory Tract

Motivated by a desire to uncover new opportunities for designing the size and shape of fiber-shaped aerosols towards improved pulmonary drug delivery deposition outcomes, we explore the transport and deposition characteristics of fibers under physiologically inspired inhalation conditions in silico, mimicking a dry powder inhaler (DPI) maneuver in adult lung models. Here, using computational fluid dynamics (CFD) simulations, we resolve the transient translational and rotational motion of inhaled micron-sized ellipsoid particles under the influence of aerodynamic (i.e., drag, lift) and gravitational forces in a respiratory tract model spanning the first seven bifurcating generations (i.e., from the mouth to upper airways), coupled to a more distal airway model representing nine generations of the mid-bronchial tree. Aerosol deposition efficiencies are quantified as a function of the equivalent diameter (dp) and geometrical aspect ratio (AR), and these are compared to outcomes with traditional spherical particles of equivalent mass. Our results help elucidate how deposition patterns are intimately coupled to dp and AR, whereby high AR fibers in the narrow range of dp = 6-7 µm yield the highest deposition efficiency for targeting the upper- and mid-bronchi, whereas fibers in the range of dp= 4-6 µm are anticipated to cross through the conducting regions and reach the deeper lung regions. Our efforts underscore previously uncovered opportunities to design the shape and size of fiber-like aerosols towards targeted pulmonary drug delivery with increased deposition efficiencies, in particular by leveraging their large payloads for deep lung deposition.

Association Between Serum Testosterone and Serum PSA Among Men With and Without Partial Androgen Deficiency

Serum prostatic specific antigen (PSA) and serum testosterone levels share an undefined relationship with each other, with many conflicting studies showing both positive and negative correlation between them. Our aim was to assess association between serum PSA and serum testosterone in healthy men with normal testosterone levels and men with partial androgen deficiency (PADAM). A cross sectional study was conducted at a teaching hospital setting where serum testosterone and aging male symptom scale (AMS) scores along with PSA were studied in 255 men (> 50 years) with and without PADAM. Mean total testosterone and serum PSA was 9.35 ± 1.33 nmol/L, 1.96 ± 0.76 ng/mL in males with PADAM and 15.30 ± 1.95 nmol/L, 1.85 ± 0.73 ng/mL respectively in males without PADAM. No significant relationship was observed between serum PSA and serum testosterone levels among healthy males irrespective of PADAM in the study population. We suggest, there is no need to adjust PSA values for biopsy decisions according to testosterone levels.

Paraneoplastic Cerebellar Degeneration in Nasopharyngeal Carcinoma: a Unique Association

Paraneoplastic cerebellar degeneration (PCD) is a rare disorder that is associated with lung or gynecological malignancies and Hodgkin lymphoma. Neurologic symptoms are commonly the initial presenting sign leading to the diagnosis of an underlying malignancy. We are presenting an Asian male with progressive lower extremity weakness with EBV-positive nasopharyngeal carcinoma (NPC) and anti-Yo antibodies. Peculiarly, transient diffuse leptomeningeal enhancement is seen on MR imaging. This is the first report of PCD associated with NPC and thus illustrates that PCD embodies a boarder set of disease than previously described.

Posttransplant Lymphoproliferative Disorder: Experience from a Pediatric Nephrology Unit in North India

Posttransplant lymphoproliferative disorder (PTLD) is reported in 1%–3% among pediatric renal allograft recipients. We report the experience of PTLD among pediatric renal allograft recipients at a pediatric nephrology center in North India. Four cases of PTLD were identified from among records of 95 pediatric renal allograft recipients over a period of 21 years. Constitutional and localizing symptoms were present in three patients each. The diagnosis was suggested on positron emission tomography in three patients and confirmed by histopathology in all. Sites affected included tonsils, cervical lymph nodes, duodenum, and para-aortic lymph nodes in one patient each. The lymphocytic infiltrate was polymorphic in three patients and monomorphic in one. Immunostaining suggested B-cell origin in all patients. There was evidence of Epstein–Barr virus infection in only one patient. The patients were successfully managed with reduction of immunosuppression (in all), rituximab (in 3), and excision of affected tissue (in 1). Over a follow-up period of 30–88 months, there were no episodes of disease recurrence or allograft rejection, and renal function was preserved.

Primary Tubercular Granulomatous Thyroiditis, Presenting as Thyroid Nodule with Hyperthyroidism, Pyrexia of Unknown Origin and Severe Anemia

Tuberculosis of Thyroid gland is a rare entity even in countries with high prevalence of tuberculosis. The patients present with a broad spectrum of manifestations ranging from an isolated painful nodule to frank hyperthyroidism. We report an interesting case of primary tubercular granulomatous thyroiditis, presenting as a thyroid nodule with pyrexia of unknown origin, hyperthyroidism and severe anaemia which responded to anti tubercular and anti-inflammatory treatment with complete recovery, as evidenced by blood reports and CT scan reports. Thus, proper diagnosis may avoid unnecessary surgical interventions, that were a trend in the past.

Multi-organ IgG4-related disease: Demystifying the diagnostic enigma

IgG4-related disease (IgG4-RD) is a multisystemic mass forming immune-mediated disease entity, commonly creating confusion and diagnostic challenges. We present a case of a 25-year-old female who presented with bilateral orbital masses, lymphadenopathy, paraspinal and renal masses, which clinicoradiologically simulated lymphoma. The lymph node biopsy revealed interfollicular sheets of plasma cells creating confusion with Castleman's disease and marginal zone lymphoma. The orbital biopsy revealed ductular destruction, periductular plasma cells, and fibrosis, mimicking Sjogren's syndrome and Castleman's disease. However, the correlation of the clinical features with histopathological findings, IgG4 immunopositivity, and serum studies helped in clinching the diagnosis. This case presents an uncommon combination of clinical features infrequently reported in literature. Furthermore, and more importantly, it highlights the need to keep a differential of IgG4-RD in mind, to aid early and correct treatment of the disease.

Association of Vitamin D Levels and type 2 Diabetes Mellitus in Asian Indians is Independent of Obesity

Background A large proportion of subjects with type 2 diabetes mellitus (T2DM) in India are non-obese. Asian-Indian subjects with diabetes have been shown to have low vitamin D levels. Whether low vitamin D levels and T2DM in Asian-Indians is attributable to the associated obesity as in caucasians is unclear. Hence we studied the association of vitamin D levels and T2DM in Asian-Indians with or without obesity.

Methods Total of 213 subjects were recruited in four groups, group 1-Non-obese diabetic, group 2-Non-obese non-diabetic, group 3-Obese diabetic and group 4-Obese non-diabetic. Subjects recruited under various groups were matched for age and sex. Anthropometry, skin-fold thickness, fasting and postprandial plasma glucose, HbA1c, fasting insulin, lipids and vitamin D levels were measured in all study subjects and were compared between the groups.

Results Mean age of study population was 41.23±7.43 years. Mean BMI in groups 1,2,3 and 4 was 21.34±1.41, 20.53±2.27, 27.72±2.94 and 27.62±3.37 kg/m2 respectively. Overall 64.3% study subjects had vitamin D deficiency and 27.7% had insufficient vitamin D levels. Significantly lower vitamin D levels were found in diabetic groups 1 and 3 compared to non-diabetic groups 2 and 4. No significant difference was observed in vitamin D levels between groups 1 and 3. Similarly, no significant difference was observed in vitamin D levels between groups 2 and 4. Vitamin D levels did not show any significant correlation with BMI, waist or body fat.

Conclusion Vitamin D levels do not appear to be related to obesity in diabetic as well non-diabetic Asian-Indian individuals.

Serial perioperative cell-free DNA levels in donors and recipients undergoing living donor liver transplantation

BACKGROUND

Effect of anaesthesia and surgery on cell-free DNA (cfDNA) is not known. Given that surgical stress augments inflammation and injury, we hypothesized that levels of cfDNA will fluctuate during perioperative period. Therefore, in this study serial perioperative cfDNA concentration was measured in donors and recipients undergoing living donor liver transplantation (LDLT).

METHODS

Baseline, post-induction, intraoperative and post-operative plasma cfDNA levels were evaluated in 21 donors and recipients each, by Sytox green method. In addition, qPCR was performed in a subset of samples.

RESULTS

Baseline cfDNA levels were higher in recipients (37.62 ng/ml) than in donors (25.49 ng/ml). A decrease in cfDNA was observed following anaesthesia induction in both recipients (11.90 ng/ml) and donors (10.75 ng/ml). When the kinetics of the cfDNA was monitored further, an increase was noted intraoperatively in donors (46.18 ng/ml) and recipients (anhepatic phase: 56.25 ng/ml, reperfusion phase: 54.36 ng/ml). cfDNA levels remained high post-operatively. One recipient who developed post-operative sepsis had the highest cfDNA level (94.72 ng/ml).

CONCLUSION

Plasma cfDNA levels are high in recipients indicative of liver injury. Lower cfDNA levels following induction may be attributed to the subduing effect of anaesthetic agents on cell death. High cfDNA levels seen in intra- and post-operative phases reflect cellular trauma and inflammation. This similar pattern of fluctuation of cfDNA level in donors and recipients is suggestive of its possible utility as a surgical stress marker. In addition, comparable cfDNA levels in anhepatic and reperfusion phase reflect less ischemia reperfusion injury during LDLT.

Feature Extraction Methods for Speaker Recognition: A Review

This paper presents main paradigms of research for feature extraction methods to further augment the state of art in speaker recognition (SR) which has been recognized extensively in person identification for security and protection applications. Speaker recognition system (SRS) has become a widely researched topic for the last many decades. The basic concept of feature extraction methods is derived from the biological model of human auditory/vocal tract system. This work provides a classification-oriented review of feature extraction methods for SR over the last 55 years that are proven to be successful and have become the new stone to further research. Broadly, the review work is dichotomized into feature extraction methods with and without noise compensation techniques. Feature extraction methods without noise compensation techniques are divided into following categories: On the basis of high/low level of feature extraction; type of transform; speech production/auditory system; type of feature extraction technique; time variability; speech processing techniques. Further, feature extraction methods with noise compensation techniques are classified into noise-screened features, feature normalization methods, feature compensation methods. This classification-oriented review would endow the clear vision of readers to choose among different techniques and will be helpful in future research in this field.

Inscription of type I and depressed cladding waveguides in lithium niobate using a femtosecond laser

We describe two types of waveguides (type I and depressed cladding) inscribed in lithium niobate using a variable repetition rate (200 kHz-25 MHz), 270 fs duration fiber laser. The type I modification-based waveguides have propagation losses in the range from 1.2 to 10 dB/cm at 1550 nm, depending on experimental parameters. These waveguides are not permanent; they deteriorate over time. Such deterioration of waveguides can be slowed down from 30 days to 100 days by pre-annealing the samples and by writing at a 720 kHz laser repetition rate. The propagation losses measured at 1550 nm show significant improvement for pre-annealed samples. The depressed cladding-inscribed waveguides are permanent, but the propagation loss depends on the number of damage tracks. A track separation of ∼1  μm between adjacent damage tracks yields the lowest propagation loss of 0.5 dB/cm at 1550 nm for a 40 μm diameter waveguide. We observe multimode guidance for sizes in the range of 20-80 μm in these waveguide structures at 1550 nm. Their crystalline nature is found to remain intact, as inferred from second-harmonic generation within the waveguide region.

Potential of native shrubs Haloxylon salicornicum and Calligonum Polygonoides for restoration of degraded lands in Arid Western Rajasthan, India

Shrub-induced soil property spatial heterogeneity is common in arid and semi-arid ecosystems and aids desertified land restoration. However, the effectiveness of this technique may rely on the plant species used and the habitat conditions present. To assess the degree to which planting two native species, Haloxylon salicornicum and Calligonum polygonoides, facilitates degraded land restoration, soil and herbaceous plant community properties were measured 7 years after planting. Soil samples were extracted at two depths (0-5 and 5-20 cm) from three sub-habitats, i.e., under the shrub canopy, from alleys between shrubs and from the open area. Shrub planting increased the quantity of silt + clay content (30-39 %); enhanced water holding capacities (24-30 %); increased the levels of organic carbon (48-69 %), available nitrogen (31-47 %), available phosphorus (32-41 %), and electrical conductivity (21-33 %); and decreased the pH (7-12 %) and bulk density levels (5-6 %) in the surface layer of soils beneath the canopy. Soil property changes were more significant at the surface (0-5 cm) than in the deeper layer (5-20 cm), and were more pronounced under H. salicornicum than under C. polygonoides. Furthermore, the density and biomass levels of herbaceous plants were 1.1 to 1.2 and 1.4 to 1.6 times greater, respectively, in the shrub alleys than in open area. H. salicornicum induced more robust soil amelioration and herbaceous plant facilitative properties than did C. polygonoides. Artificially planting these shrubs may thus be employed to restore degraded areas of arid regions.

Structural, magnetic, and dielectric studies on Gd0.7Y0.3MnO3

Structural, magnetic, specific heat, and dielectric studies were carried out on Y substituted (30 at. %) GdMnO(3) compound as a function of temperature. Anomalies occur at ~41 and 18 K, in the specific heat measurements and are ascribed to paramagnetic, to sinusoidal incommensurate antiferromagnetic transition (ICAFM) and ICAFM to commensurate antiferromagnetic transitions, respectively. Changes in the lattice parameters across these temperatures indicate magneto-elastic coupling present in the compound. However, in the dielectric measurements, an anomaly at 18 K alone is observed and is ascribed to a ferroelectric transition, giving rise to spontaneous ferroelectric ordering at low temperatures. This observation is supported by an anomaly in lattice parameters, across the transition temperature. From the frequency dependent dielectric studies, a strong coupling between Gd(3+) and Mn(3+) magnetic sublattices is inferred and Y substitution results in substantial changes in the relaxation process compared to that of GdMnO(3).

Spin-valve-like magnetoresistance in Mn2NiGa at room temperature

Spin valves have revolutionized the field of magnetic recording and memory devices. Spin valves are generally realized in thin film heterostructures, where two ferromagnetic (FM) layers are separated by a nonmagnetic conducting layer. Here, we demonstrate spin-valve-like magnetoresistance at room temperature in a bulk ferrimagnetic material that exhibits a magnetic shape memory effect. The origin of this unexpected behavior in Mn(2)NiGa has been investigated by neutron diffraction, magnetization, and ab initio theoretical calculations. The refinement of the neutron diffraction pattern shows the presence of antisite disorder where about 13% of the Ga sites are occupied by Mn atoms. On the basis of the magnetic structure obtained from neutron diffraction and theoretical calculations, we establish that these antisite defects cause the formation of FM nanoclusters with parallel alignment of Mn spin moments in a Mn(2)NiGa bulk lattice that has antiparallel Mn spin moments. The direction of the Mn moments in the soft FM cluster reverses with the external magnetic field. This causes a rotation or tilt in the antiparallel Mn moments at the cluster-lattice interface resulting in the observed asymmetry in magnetoresistance.