Prognostic value of hematological parameters in older adult patients with acute coronary syndrome undergoing coronary intervention: a single centre prospective study.

BACKGROUND: Cardiovascular disease is a significant contributor to the disease burden in geriatric patients. Underlying systemic inflammation is thought to be the cause of age-related changes in the bone marrow and a major risk factor for atherosclerosis. The purpose of the study was to assess the accuracy of these hematological biomarkers in predicting 30-day mortality in older patients with acute coronary syndrome (ACS). METHODS: This was a prospective observational study of 601 older adult patients (age > 60 years) with ACS who underwent percutaneous coronary intervention over two years (2017-2019). The relationship between baseline hematological parameters and mortality was assessed during the 30-day follow-up. Logistic regression analysis and receiver operating characteristic curve analysis were done to evaluate for diagnostic accuracy of various hematological parameters. RESULTS: The mean age of presentation was 77 ± 17 years. The mean neutrophil-lymphocyte ratio (NLR) value was 5.07 ± 4.90 and the mean platelet-lymphocyte ratio (PLR) value was 108.65 ± 85.82. On univariate analysis, total leucocyte count [odds ratio (OR) = 0.85, P = 0.021], hematocrit (OR = 0.91, P = 0.018), NLR (OR = 1.10, P = 0.001) and PLR (OR = 1.05, P = 0.001) were associated with mortality. On receiver operating characteristic curve analysis, NLR predicted mortality with 68.1% and PLR with 65.7% accuracy. On multivariate analysis, NLR (OR = 1.096, 95% CI: 1.006-1.15, P = 0.035) was an independent predictor of 30-day mortality. CONCLUSIONS: For the risk classification of all elderly ACS patients, we highly advise using NLR rather than the total white blood cell count.

Clinicopathological Features and Status of Programmed Death Ligand-1 (PD-L1) Expression in Lung Cancer: A Single Centre Study From North India.

Introduction Programmed death ligand-1 (PD-L1) is an immunological checkpoint that supports the inhibition of the anti-tumor immune system. A higher level of PD-L1 expression was also discovered on the cell surfaces of several cancer cells, including non-small cell lung carcinoma (NSCLC). Identifying individuals who would benefit from PD-1/PD-L1 antibody immunotherapy is crucial in the era of precision medicine. The study's objective was to assess the distribution and degree of PD-L1 ligand expression in various forms of lung cancer and examine its link to clinicopathological variables. Methods This prospective, observational, cross-sectional study was done in a tertiary care hospital in North India over 2 years from 2019 to 2021. A total of 100 patients diagnosed with lung cancer through either endobronchial or image-guided biopsies were enrolled. The biopsy specimens of lung cancer patients have been subjected to immunohistochemistry (IHC) staining. PD-L1 expression was positive when at least 1% of tumor cells were stained. In our study, we used the rabbit monoclonal Anti-PD-L1 antibody (CAL10) (ab237726) (Abcam Plc, UK).  Results  Of the 100 patients, Squamous cell carcinoma (SQCC) was the predominant histological pattern. The mean age of the study group was 57.26 ± 10.53 years. High PDL-1 positivity (>50% ) is seen in a total of 10 patients, while low PD-L1 positivity (1-50%) is seen in 24 patients. Of all patients with high PD-L1 positivity (n=10), 80% had stage IV at the time of diagnosis. However, on similar lines, 71 % of patients with low PD-L1 positivity presented with stage IV at the time of diagnosis. (p value=0.09). Among 10 patients with epidermal growth factor receptor (EGFR) positive status, high PD-L1 positivity is seen in 20%. Among 3 patients with anaplastic lymphoma kinase (ALK) positive status, only one patient showed high PD-L1 positivity, whereas negative PDL-1 was seen in 2 patients, which was not statistically significant. Conclusion  The management of lung cancer is driven by precision medicine, including PDL-1 expression, which correlates with immune checkpoint inhibitor response. In our cohort, PD-L1 expression appears to be mostly linked to the squamous cell subtype of lung cancer, with elevated tumor stage and mediastinal lymphadenopathy in Kashmiri people. Other oncogenic driver mutations are not connected to PD-L1 expression. The function of PD-L1 expression in lung tumors requires more study.

The Trend of Arterial Carboxyhemoglobin in Non-smokers as a Prognostic Tool in Severe COVID-19 Patients: A Single-Centre Prospective Study.

Introduction  Carboxyhemoglobinemia is characterised by decreased oxygen delivery to tissues. In severe and critical coronavirus disease 2019 (COVID-19) illness with hypoxia, this can herald a grave and protracted course of illness. Patients with COVID-19 experience respiratory impairment, lowering the pace at which carbon monoxide (CO) is eliminated and raising the likelihood of carboxyhemoglobinemia. We set out to explore early arterial carboxyhemoglobin (COHb) and COVID-19 patient outcomes in non-smokers and its potential as a predictive tool for mortality. Methods  Forty-five patients, non-smokers with severe/critical severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection requiring admission in a North Indian 1200-bedded tertiary care hospital, were recruited prospectively from October 2020 to March 2021. Arterial COHb% was evaluated with arterial blood gases using an analyser, which were taken at the time of admission and then every alternate day for the first 10 days. Carboxyhemoglobinemia was defined as COHb% more than 1%. The primary outcome was defined as the patient's hospital outcome (survivor/non-survivor). Results Of the total 45 subjects, 51.1% (n=23) survived. Patients developed carboxyhemoglobinemia with an incidence of 51% during the course of their hospital stay. The mean ± SD of COHb% on admission was 1.0 ± 0.58 and 1.03 ± 0.8 in non-survivors and survivors, respectively (p=0.870). Maximal individual values of 5.3% and 6.1% were seen in survivors and non-survivors, respectively. On serial COHb measurement, non-survivors had significantly higher COHb% on days 6 and 10. No co-relation of COHb% with inflammatory markers was noted. Conclusion  Arterial COHb levels in non-survivors were significantly higher than in survivors on days 6 and 10. Our study did not show a prognostic value of serial COHb measurement in patients with severe COVID-19. To establish COHb as a predictive marker in severely ill COVID-19 patients, additional research is required.

Follicular Lymphoma Secondary to Chronic Myeloid Leukemia During Treatment With Imatinib.

Tyrosine kinase inhibitors (TKIs) remain the mainstay of treatment for those with chronic myeloid leukemia (CML); nonetheless, there is concern over the possibility of additional cancers as a result of TKI use. There are not many cases in the literature where tyrosine kinase treatment caused a patient to develop secondary lymphoma. Herein we present a 49-year-old male diagnosed with CML in 2014, on Imatinib for six years with a major molecular response, who presented with generalized lymphadenopathy in July 2020. The complete evaluation was done, and histopathology and immunohistochemistry revealed follicular lymphoma. He responded well to six cycles of bendamustine and rituximab treatment (BR). It is critical for treating physicians to be aware of such occurrences, and patients on TKI must be closely monitored.

A Rare Case of Brucellosis With Spontaneous Splenic Rupture Presenting as an Acute Abdomen.

Brucellosis is a common zoonotic infection worldwide caused by the bacterial species Brucella. It has a wide range of presentations from asymptomatic infection to multisystem involvement. Splenomegaly is seen in around 30-60% of cases, however, atraumatic spontaneous splenic rupture is extremely rare. We present a case of a 45-year-old man who presented with acute left upper quadrant pain and fever of five days duration without a history of antecedent trauma. He was hemodynamically stable with examination revealing left upper quadrant tender palpable mass. Ultrasonography followed by computed tomography revealed subcapsular hematoma with perisplenic and perihepatic free fluid. Viral markers (hepatitis B and C, cytomegalovirus {CMV}, Epstein-Barr virus {EBV}, HIV, and dengue) were negative. The autoimmune profile was negative. Brucella serum agglutination test was positive (1: 640) and blood cultures grew Brucella melitensis. He was managed conservatively for splenic hematoma and received one unit blood transfusion and treatment with combination of antibiotics (rifampicin and doxycycline) for brucella for six weeks. On follow-up, the patient reported no further complications. Spontaneous splenic rupture is a clinical rarity and should be considered in patients presenting with acute abdomen and suspected infective, neoplastic, and inflammatory pathology. Spontaneous splenic rupture in acute brucellosis requires prompt clinical recognition and immediate anti-Brucella therapy to prevent the catastrophic progression.

Tuberculosis of Finger Presenting As Non-healing Ulcer of Digit: A Case Report.

Tuberculosis (TB) is a chronic granulomatous infection which most often localises to the respiratory system. Extra-pulmonary tuberculosis is prevalent in immunocompromised individuals, of which cutaneous tuberculosis is exceedingly rare (0.5-2%). Cutaneous TB presents with varied clinical morphologies, either acquired exogenously via direct inoculation on the skin or endogenously due to systemic dissemination. Diagnosis is particularly challenging due to the multitude of differential diagnoses of skin lesions. Microbiological evidence from biopsy and histopathological findings suggestive of granulomatous inflammation are needed to make a definitive diagnosis. Herein we present a rare case of tuberculosis of the finger in a middle-aged man who presented with an ulcerating and erythematous lesion. As cutaneous TB is usually misdiagnosed at the earlier stages, dermatologists and primary care physicians should keep high suspicion for cutaneous TB in any non-healing ulcers which are otherwise unexplained.

Vitamin D Levels and Length of Hospitalization in Indian Patients With COVID-19: A Single-Center Prospective Study.

Introduction The role of vitamin D deficiency in increasing susceptibility or modifying outcomes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) illness is unclear, and data about the association is scant in low- and middle-income countries. We set out to investigate any correlation between baseline vitamin D status and the length of hospital stay in laboratory-confirmed SARS-CoV-2 patients in India. Methods Two hundred patients with SARS-CoV-2 infection requiring admission in a North Indian 1200-bedded tertiary care hospital were recruited prospectively from November 2020 to March 2021. Baseline serum 25 hydroxyvitamin D [25(OH)D] levels were measured within 24 hours of admission using chemiluminescent immunoassay. Patients were managed as per hospital management protocol for COVID-19. The primary outcome was the length of hospital stay; secondary outcomes were comparative clinical severity between two groups, rate of requirement of mechanical ventilation and/or non-invasive ventilation (NIV), and mortality. Vitamin D deficiency (VDD) was defined as baseline vitamin D levels of <30 ng/ml. Results  Of the 200 recruited patients, 57.5% (n = 115) patients were vitamin D deficient, and the overall median length of hospital stay was around 12 days (IQR: 8-15 days). There was no statistically significant difference in the length of hospital stay between patients with normal serum vitamin D (VDS) and those with VDD, median LOS being 12 days (95% CI: 10, 12 days) in VDD cases and 11 days (95% CI: 10,13 days) in VDS cases (p = 0.176). No association between baseline 25(OH)D and any of the secondary outcomes could be established. Conclusions In Indian patients, baseline vitamin D levels are not associated with the length of hospital stay, need for mechanical ventilation, or mortality.

Vitamin D Toxicity Presenting as Altered Mental Status in Elderly Patients.

Background and objective  Around 25-30% of elderly patients present to emergency departments (ED) with altered mental status (AMS), with hypercalcemia being one of the metabolic causes. Elderly patients, due to their multiple vulnerability factors and relative homeostenosis, are susceptible to alterations in mental state at even milder grades of hypercalcemia. There is a trend of overzealous prescription of higher doses of vitamin D in elderly patients for various ailments, which often exceeds the requirements of the patients. In this study, we aimed to establish vitamin D toxicity (VDT) as an underlying cause of AMS in elderly patients presenting to the hospital. Methods This was a descriptive case study conducted at a tertiary care university hospital in North India, from January 2015 to March 2020 for a total duration of five years. Elderly patients (aged ≥60 years) who were admitted with VDT as a cause for underlying hypercalcemia were included. The evaluation included patient history regarding the dosage of vitamin D received, route of administration, and biochemical parameters, such as serum calcium, intact parathyroid hormone (iPTH), 25-hydroxy vitamin D [25(OH)D], and albumin. All other potential causes for hypercalcemia and AMS were ruled out concurrently. Results A total of 19 patients were enrolled in the study, with a mean age of 72.3 years (range: 62-86 years). All patients had received injectable vitamin D formulation. The mean serum calcium among the patients was 12.52 ± 1.12 mg/dL (range: 11.2-15.7 mg/dL), whereas the mean 25(OH)D was 196.34 ± 70.44 ng/mL (range: 107-356 ng/mL). The mean cumulative vitamin D supplement intake was 2.594 ± 0.841 million IU (range: 1.2 million-4.2 million IU). While six patients had mild hypercalcemia, 12 had moderate, and one person had severe hypercalcemia, with altered sensorium (85%) being the most common complaint for presenting to ED, followed by generalized weakness (15%). Conclusion VDT can manifest with AMS as an initial presenting complaint. The geriatric population, due to various underlying vulnerability factors, is more susceptible than their younger counterparts. We strongly recommend that in elderly patients, higher doses of vitamin D should be prescribed only after checking their serum levels, and frequent monitoring of vitamin D should be performed.

Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection.

Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.

Development of antibody-dependent cell cytotoxicity function in HIV-1 antibodies.

A prerequisite for the design of an HIV vaccine that elicits protective antibodies is understanding the developmental pathways that result in desirable antibody features. The development of antibodies that mediate antibody-dependent cellular cytotoxicity (ADCC) is particularly relevant because such antibodies have been associated with HIV protection in humans. We reconstructed the developmental pathways of six human HIV-specific ADCC antibodies using longitudinal antibody sequencing data. Most of the inferred naive antibodies did not mediate detectable ADCC. Gain of antigen binding and ADCC function typically required mutations in complementarity determining regions of one or both chains. Enhancement of ADCC potency often required additional mutations in framework regions. Antigen binding affinity and ADCC activity were correlated, but affinity alone was not sufficient to predict ADCC potency. Thus, elicitation of broadly active ADCC antibodies may require mutations that enable high-affinity antigen recognition along with mutations that optimize factors contributing to functional ADCC activity.

Nearly four decades after the human immunodeficiency virus (HIV for short) was first identified, the search for a vaccine still continues. An effective immunisation would require elements that coax the human immune system into making HIV-specific antibodies ­ the proteins that can recognise, bind to and deactivate the virus. Crucially, antibodies can also help white blood cells to target and destroy cells infected with HIV. This 'antibody-dependent cellular cytotoxicity' could be a key element of a successful vaccine, yet it has received less attention than the ability for antibodies to directly neutralize the virus. In particular, it is still unclear how antibodies develop the ability to flag HIV-infected cells for killing. Indeed, over the course of an HIV infection, an immune cell goes through genetic changes that tweak the 3D structure of the antibodies it manufactures. This process can improve the antibodies' ability to fight off the virus, but it was still unclear how it would shape antibody-dependent cellular cytotoxicity. To investigate this question, Doepker et al. retraced how the genes coding for six antibody families changed over time in an HIV-carrying individual. This revealed that antibodies could not initially trigger antibody-dependent cellular cytotoxicity. The property emerged and improved thanks to two types of alterations in the genetic sequences. One set of changes increased how tightly the antibodies could bind to the virus, targeting sections of the antibodies that can often vary. The second set likely altered the 3D structure in others ways, potentially affecting how antibodies bind the virus or how they interact with components of the immune system that help to kill HIV-infected cells. These alterations took place in segments of the antibodies that undergo less change over time. Ultimately, the findings by Doepker et al. suggest that an efficient HIV vaccine may rely on helping antibodies to evolve so they can bind more tightly to the virus and trigger cellular cytotoxicity more strongly.

A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.

The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.

Gene Therapy for Angelman Syndrome: Contemporary Approaches and Future Endeavors.

BACKGROUND: Angelman Syndrome (AS) is a congenital non inherited neurodevelopmental disorder. The contemporary AS management is symptomatic and it has been accepted that gene therapy may play a key role in the treatment of AS. OBJECTIVE: The purpose of this study is to summarize existing and suggested gene therapy approaches to Angelman syndrome. METHODS: This is a literature review. Pubmed and Scopus databases were researched with keywords (gene therapy, Angelman's syndrome, neurological disorders, neonates). Peer-reviewed studies that were closely related to gene therapies in Angelman syndrome and available in English, Greek, Ukrainian or Indonesian were included. Studies that were published before 2000 were excluded and did not align with the aforementioned criteria. RESULTS: UBE3A serves multiple roles in signaling and degradation procedures. Although the restoration of UBE3A expression rather than targeting known activities of the molecule would be the optimal therapeutic goal, it is not possible so far. Reinstatement of paternal UBE3A appears as an adequate alternative. This can be achieved by administering topoisomerase-I inhibitors or reducing UBE3A antisense transcript (UBE3A-ATS), a molecule which silences paternal UBE3A. CONCLUSION: Understanding UBE3A imprinting unravels the path to an etiologic treatment of AS. Gene therapy models tested on mice appeared less effective than anticipated pointing out that activation of paternal UBE3A cannot counteract the existing CNS defects. On the other hand, targeting abnormal downstream cell signaling pathways has provided promising rescue effects. Perhaps, combined reinstatement of paternal UBE3A expression with abnormal signaling pathways-oriented treatment is expected to provide better therapeutic effects. However, AS gene therapy remains debatable in pharmacoeconomics and ethics context.

Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage.

HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.

Predicting B cell receptor substitution profiles using public repertoire data.

B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e. in the same "clonal family") are released from the germinal center; their amino acid frequency profile reflects the allowed and disallowed substitutions at each position. These clonal-family-specific frequency profiles, called "substitution profiles", are useful for studying the course of affinity maturation as well as for antibody engineering purposes. However, most often only a single sequence is recovered from each clonal family in a sequencing experiment, making it impossible to construct a clonal-family-specific substitution profile. Given the public release of many high-quality large B cell receptor datasets, one may ask whether it is possible to use such data in a prediction model for clonal-family-specific substitution profiles. In this paper, we present the method "Substitution Profiles Using Related Families" (SPURF), a penalized tensor regression framework that integrates information from a rich assemblage of datasets to predict the clonal-family-specific substitution profile for any single input sequence. Using this framework, we show that substitution profiles from similar clonal families can be leveraged together with simulated substitution profiles and germline gene sequence information to improve prediction. We fit this model on a large public dataset and validate the robustness of our approach on two external datasets. Furthermore, we provide a command-line tool in an open-source software package (https://github.com/krdav/SPURF) implementing these ideas and providing easy prediction using our pre-fit models.

Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time.

Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the evolutionary process on the phylogeny and, unlike parsimony-based mapping, conditions on the observed data to randomly draw substitution mappings that do not necessarily require the minimum number of events on a tree. Most stochastic mapping applications simulate substitution mappings only to estimate the mean and/or variance of two commonly used mapping summaries: the number of particular types of substitutions (labeled substitution counts) and the time spent in a particular group of states (labeled dwelling times) on the tree. Fast, simulation-free algorithms for calculating the mean of stochastic mapping summaries exist. Importantly, these algorithms scale linearly in the number of tips/leaves of the phylogenetic tree. However, to our knowledge, no such algorithm exists for calculating higher-order moments of stochastic mapping summaries. We present one such simulation-free dynamic programming algorithm that calculates prior and posterior mapping variances and scales linearly in the number of phylogeny tips. Our procedure suggests a general framework that can be used to efficiently compute higher-order moments of stochastic mapping summaries without simulations. We demonstrate the usefulness of our algorithm by extending previously developed statistical tests for rate variation across sites and for detecting evolutionarily conserved regions in genomic sequences.