Nevin Manimala

Neural Netw. 2021 Dec 30;147:186-197. doi: 10.1016/j.neunet.2021.12.017. Online ahead of print.

ABSTRACT

This paper proposes an Information Bottleneck theory based filter pruning method that uses a statistical measure called Mutual Information (MI). The MI between filters and class labels, also called Relevance, is computed using the filter’s activation maps and the annotations. The filters having High Relevance (HRel) are considered to be more important. Consequently, the least important filters, which have lower Mutual Information with the class labels, are pruned. Unlike the existing MI based pruning methods, the proposed method determines the significance of the filters purely based on their corresponding activation map’s relationship with the class labels. Architectures such as LeNet-5, VGG-16, ResNet-56, ResNet-110 and ResNet-50 are utilized to demonstrate the efficacy of the proposed pruning method over MNIST, CIFAR-10 and ImageNet datasets. The proposed method shows the state-of-the-art pruning results for LeNet-5, VGG-16, ResNet-56, ResNet-110 and ResNet-50 architectures. In the experiments, we prune 97.98%, 84.85%, 76.89%, 76.95%, and 63.99% of Floating Point Operation (FLOP)s from LeNet-5, VGG-16, ResNet-56, ResNet-110, and ResNet-50 respectively. The proposed HRel pruning method outperforms recent state-of-the-art filter pruning methods. Even after pruning the filters from convolutional layers of LeNet-5 drastically (i.e., from 20, 50 to 2, 3, respectively), only a small accuracy drop of 0.52% is observed. Notably, for VGG-16, 94.98% parameters are reduced, only with a drop of 0.36% in top-1 accuracy. ResNet-50 has shown a 1.17% drop in the top-5 accuracy after pruning 66.42% of the FLOPs. In addition to pruning, the Information Plane dynamics of Information Bottleneck theory is analyzed for various Convolutional Neural Network architectures with the effect of pruning. The code is available at https://github.com/sarvanichinthapalli/HRel.

PMID:35042156 | DOI:10.1016/j.neunet.2021.12.017

Semin Arthritis Rheum. 2021 Dec 31;52:151937. doi: 10.1016/j.semarthrit.2021.11.008. Online ahead of print.

ABSTRACT

OBJECTIVE: To investigate the association between timing of respiratory tract diseases and risk of rheumatoid arthritis (RA).

METHODS: This case-control study using the Mass General Brigham Biobank matched incident RA cases, confirmed by ACR/EULAR criteria, with at least seven years preceding electronic health record (EHR) data to three controls on age, sex, and EHR history from RA diagnosis (index date). We ascertained timing (>0-5 years/>5-10 years/>10 years) of the first documented respiratory tract disease prior to index date using diagnosis codes. We estimated odds ratios (OR) with 95% confidence intervals (CI) for RA for each respiratory exposure using logistic regression models, adjusting for potential confounders. We also conducted a stratified analysis by serostatus and smoking.

RESULTS: We identified 625 incident RA cases (median 56 years, 75% female, 57% seropositive) and 1,875 controls. Acute sinusitis was associated with RA only in the >5 to 10 years before RA (OR 3.90, 95% CI:1.90,8.01). In contrast, pneumonia was associated with RA only in the >0 to 5 years before RA (OR 1.73, 95% CI:1.00,3.00), and chronic respiratory tract diseases only >10 years before RA (OR 1.43, 95% CI:1.00,2.05). All respiratory tract diseases tended to show a stronger association with seronegative RA than seropositive RA, although the interaction was statistically significant only for chronic sinusitis (p=0.04). Respiratory diseases showed a nonsignificantly stronger association among smokers than nonsmokers.

CONCLUSION: Sinusitis and other respiratory diseases are associated with increased risk of RA, especially 5 years before RA onset. RA may begin many years before clinical onset.

PMID:35042150 | DOI:10.1016/j.semarthrit.2021.11.008

Cancer Epidemiol. 2022 Jan 15;77:102089. doi: 10.1016/j.canep.2021.102089. Online ahead of print.

ABSTRACT

OBJECTIVE: We studied 5-year relative survival (RS) for 14 leading cancer sites in the population-based cancer registry (PBCR) of Golestan province in the northeastern part of Iran.

METHODOLOGY: We followed patients diagnosed in 2007-2012 through data linkage with different databases, including the national causes of death registry and vital statistics office. We also followed the remaining patients through active contact. We used relative survival (RS) analysis to estimate 5-year age-standardized net survival for each cancer site. Multiple Imputation (MI) method was performed to obtain vital status for loss to follow-up (LTFU) cases.

RESULTS: We followed 6910 cancer patients from Golestan PBCR. However, 2162 patients were loss to follow-up. We found a higher RS in women (29.5%, 95% CI, 27.5, 31.7) than men (21.0%, 95% CI, 19.5, 22.5). The highest RS was observed for breast cancer in women (RS=49.8%, 95% CI, 42.2, 56.9) and colon cancer in men (RS=37.9%, 95% CI, 31.2, 44.6). Pancreatic cancer had the lowest RS both in men (RS= 8.7%, 95% CI, 4.1, 13.5) and women (RS= 7.9%, 95% CI, 5.0, 10.8) CONCLUSION: Although the 5-year cancer survival rates were relatively low in the Golestan province, there were distinct variations by cancer site. Further studies are required to evaluate the survival trends in Golestan province over time and compare them with the rates in the neighboring provinces and other countries in the region.

PMID:35042146 | DOI:10.1016/j.canep.2021.102089

J Pharm Biomed Anal. 2022 Jan 6;210:114585. doi: 10.1016/j.jpba.2022.114585. Online ahead of print.

ABSTRACT

Thermal analysis, Fourier Transform IR, the isotropic chemical shift of ¹H NMR in different solvents, their temperature dependence and spin-lattice relaxation time constant (T₁), solution 1D and 2D NMR, and solid-state ¹³C and ³¹P NMR (magic angle spinning NMR) were employed to obtain full information and elucidate the structures of primaquine diphosphate (PQD) samples used for quality controlling malaria medicines. Additionally, a simple, rapid, specific, and reliable quantitative method (qNMR) was developed to determine the PQD level in the raw material of active pharmaceutical ingredients (APIs). The method was developed using ethylene carbonate (EC) as the internal standard and dimethylsulfoxide-d₆ (DMSO-d₆) as the NMR solvent. For the API qNMR, ¹H NMR signals at 3.82 and 1.22 ppm were used. The qNMR methodology, through the linearity, range, LOD and LOQ, stability, precision, robustness, and accuracy, was validated within the requirements of guidelines. The accuracy of the qNMR was evaluated by comparing it to a pharmacopeial HPLC technique and there were no statistical differences (p > 0.05). The proposed qNMR method authentically supports and endorses the current pharmacopoeial methods used for determining the PQD content.

PMID:35042143 | DOI:10.1016/j.jpba.2022.114585

Animal. 2022 Jan 13;16(2):100446. doi: 10.1016/j.animal.2021.100446. Online ahead of print.

ABSTRACT

Over the last decades, permanent crating of farrowing and lactating sows has led to serious public concerns with regard to sow welfare. As one alternative, it has been suggested to restrict crating to the period when suckling piglets are at the highest risk to die. Therefore, the aim of this study was to investigate live-born piglet mortality with regard to different confinement periods (CFP) as well as farrowing pen types. On three research farms (A, B and C), four confinement periods were compared: In CFP 0 (control), sows were not confined at all, sows in CFP 3 were crated after the end of farrowing for three days. In CFP 4, sows were confined one day before the due date of farrowing until three days after parturition and sows in CFP 6 were crated one day before expected farrowing until five days after parturition. Furthermore, five different pen types designed for temporary crating (PT; 5.5-7.3 m²) were compared. In total, production data from 638 litters were analysed. For each piglet found dead (n = 1 580), the cause of death was determined by the farm personnel and verified by necropsy (all three farms) and additional video analysis (farms A and B only). Data were analysed using logistic mixed models with CFP 0 and pen type Fluegel as reference categories (CFP 0 was control and this pen type was present on all three farms and the largest number of litters was born in this pen type). Live-born piglet mortality was lower in temporarily crated sows than in sows without confinement (CFP 0; P < 0.015). Pairwise posthoc tests did not reveal differences between CFP 3, CFP 4 and CFP 6 (odds ratios 0.75, 0.59 and 0.69), nor between pen types. Additional factors associated with increasing live-born piglet mortality were larger litter size, higher sow parity as well as the administration of hormones around farrowing. Factors influencing mortality due to crushing were similar to those for total live-born mortality with the exception of CFP 3 not differing significantly from CFP 0. It can be concluded, that confinement of the sow for three days after farrowing is an effective measure to reduce live-born piglet mortality in the pen types tested. An extension of the confinement period to five days after parturition does not result in a further reduction of live-born mortality rate.

PMID:35042138 | DOI:10.1016/j.animal.2021.100446

Prev Vet Med. 2022 Jan 5;200:105569. doi: 10.1016/j.prevetmed.2022.105569. Online ahead of print.

ABSTRACT

Fasciolosis caused by the trematode Fasciola hepatica is an important parasitosis in both livestock and humans across the globe. Chronic infections in cattle are associated with considerable economic losses. As a prerequisite for an effective control and prevention of fasciolosis in cattle fine-scale predictive models on farm-level are needed. Since disease transmission will only occur where the mollusc intermediate host is present, the objective of our research was to develop a regression model that allows to predict the local presence or absence of Galba truncatula as principal intermediate host for Fasciola hepatica in Switzerland. By implementing generalized linear mixed models (GLMMs) a total amount of 70 variables were analysed for their potential influence on the likelihood π_i of finding Galba truncatula at a certain site. Important site-specific features could be considered by selecting suitable modelling procedures. The statistical software R was used to conduct regression analysis, performing the grplasso and the glmmLasso method. The selection of parameters was based on 10-fold cross validation and the Bayesian Information Criterion (BIC). This yielded a total number of 19 potential predictor variables for the grplasso and 13 variables for the glmmLasso model, which also included random effects. Nine variables appeared to be relevant predictors for the occurrence of Galba truncatula in both models. These included reed/humid area, spring water, water bodies within a 100 m radius, and trees/bushes as powerful positive predictors. High soil depth, temperatures frequently exceeding 30 °C in the year preceding the search for snails and temperatures below 0 °C especially in the second year before were identified to exert an adverse effect on the occurrence of Galba truncatula. Temperatures measured near ground level proved to be more powerful predictors than macroclimatic parameters. Precipitation values seemed to be of minor impact in the given setting. Both regression models may be convenient for a fine-scale prediction of the occurrence of Galba truncatula, and thus provide useful approaches for the development of future spatial transmission models, mapping the risk of fasciolosis in Switzerland on farm-level.

PMID:35042123 | DOI:10.1016/j.prevetmed.2022.105569

Cell Physiol Biochem. 2022 Jan 19;56(1):13-27. doi: 10.33594/000000491.

ABSTRACT

BACKGROUND/AIMS: Waterpipe smoke (WPS) is the second most prevalent form of smoking in the world. There are ample evidences about the vascular alterations caused by regular WPS (Reg-WPS). Nonetheless, comparison of the chronic vascular response induced by regular versus occasional WPS (Occ-WPS) exposure is very scarce.

METHODS: We investigated, in BALB/c mice, the effects of Occ-WPS (30 minutes/day, 1 day/week) versus Reg-WPS (30 minutes/day, 5 days/week) for 6 months on thrombogenicity and platelet aggregation in vivo and in vitro. Moreover, various markers of endothelial integrity, inflammation and oxidative stress were assessed by enzyme-linked immunosorbent assay and colorimetric assay. Control mice were exposed to air.

RESULTS: Our results showed that either Occ-WPS or Reg-WPS exposure shortened the thrombotic time in pial microvessels in vivo. Moreover, in pial venules, this effect was more marked in Reg-WPS group (-47%) compared with Occ-WPS (-34%). Similarly, exposure to either Occ-WPS or Reg-WPS reduced the prothrombin time and activated partial thromboplastin time. Platelet count was increased only in Reg-WPS exposure. Exposure to either Occ-WPS or Reg-WPS induced platelet aggregation in vitro. In addition, there was a statistically significant difference between Occ-WPS and Reg-WPS groups in platelet count and aggregation. Plasma concentration of tissue factor (+98%), P-selectin (+14%) and E-selectin (+16%) were significantly increased in Occ-WPS group compared with air exposed group. Likewise, compared with air group Reg-WPS caused an increase in concentration of tissue factor (+193%), P-selectin (+21%) and E-selectin (+42%). Nevertheless, only Reg-WPS induced a decrease (-38%) in the plasma concentration of tissue plasminogen activator. Notably, our results showed a statistically significant difference between Occ-WPS and Reg-WPS groups in the concentration of tissue factor. Erythrocyte numbers, hemoglobin concentration, hematocrit and lactate dehydrogenase activity were augmented only in Reg-WPS group compared with either control or Occ-WPS groups. Likewise, only Reg-WPS induced an increase in proinflammatory cytokines, tumor necrosis factor-α and interleukin-1β compared with either control or Occ-WPS groups. However, markers of oxidative stress including 8-isoprostane and total antioxidants were enhanced in both Occ-WPS and Reg-WPS compared with control group.

CONCLUSION: Our data confirm the vascular toxicity of the chronic Reg-WPS exposure and shows that even occasional chronic exposure to WPS caused thrombosis, platelet aggregation, endothelial alterations and oxidative stress. The latter findings are an additional cause of concern about the long-term toxicity of occasional waterpipe smoking.

PMID:35041781 | DOI:10.33594/000000491

J Int AIDS Soc. 2022 Jan;25(1):e25863. doi: 10.1002/jia2.25863.

ABSTRACT

INTRODUCTION: There is a growing population of children who are HIV-exposed and uninfected (HEU) with the successful expansion of antiretroviral therapy (ART) use in pregnancy. Children who are HEU are at risk of delayed neurodevelopment; however, there is limited research on early brain growth and maturation. We aimed to investigate the effects of in utero exposure to HIV/ART on brain structure of infants who are HEU compared to HIV-unexposed (HU).

METHODS: Magnetic resonance imaging using a T2-weighted sequence was undertaken in a subgroup of infants aged 2-6 weeks enrolled in the Drakenstein Child Health Study birth cohort, South Africa, between 2012 and 2015. Mother-child pairs received antenatal and postnatal HIV testing and ART per local guidelines. We compared subcortical and total grey matter volumes between HEU and HU groups using multivariable linear regression adjusting for infant age, sex, intracranial volume and socio-economic variables. We further assessed associations between brain volumes with maternal CD4 cell count and ART exposure.

RESULTS: One hundred forty-six infants (40 HEU; 106 HU) with high-resolution images were included in this analysis (mean age 3 weeks; 50.7% male). All infants who were HEU were exposed to ART (88% maternal triple ART). Infants who were HEU had smaller caudate volumes bilaterally (5.4% reduction, p < 0.05) compared to HU infants. There were no group differences in other subcortical volumes (all p > 0.2). Total grey matter volume was also reduced in infants who were HEU (2.1% reduction, p < 0.05). Exploratory analyses showed that low maternal CD4 cell count (<350 cells/mm³ ) was associated with decreased infant grey matter volumes. There was no relationship between timing of ART exposure and grey matter volumes.

CONCLUSIONS: Lower caudate and total grey matter volumes were found in infants who were HEU compared to HU in the first weeks of life, and maternal immunosuppression was associated with reduced volumes. These findings suggest that antenatal HIV exposure may impact early structural brain development and improved antenatal HIV management may have the potential to optimize neurodevelopmental outcomes of children who are HEU.

PMID:35041774 | DOI:10.1002/jia2.25863

Electrophoresis. 2022 Jan 18. doi: 10.1002/elps.202100233. Online ahead of print.

ABSTRACT

Since their discovery in 2004, carbon dots (CDs) have attracted attention due to their intrinsic physicochemical properties and the easy synthesis from simple precursors. However, quantification of CDs in mixtures of nanoparticles with similar sizes and surface functionality is still a challenging issue for research applications or regulatory purposes. In this work, CDs and silver nanoparticles were firstly synthesized under alkaline conditions by using glucose as precursor and capping agent, respectively. Mixtures of these nanoparticles were made at micromolar range, without purification, and then analyzed by capillary electrophoresis-diode array detection (CE-DAD), using an electrolyte solution composed by 20 mM sodium borate and 20 mM sodium dodecylsulfate (SDS) at pH 8.5, in a total time lower than 15 min. The three-way electrophoretic data was then decomposed by advanced chemometric models, parallel factor analysis (PARAFAC) and multivariate curve resolution-alternating least-squares (MCR-ALS). The explained variances for both models were 95.8% (PARAFAC) and 85.3% (MCR-ALS). In both cases, the quality of the results was verified by the Root Mean Square Standard Deviation Coefficient Variation (RMSCV), which resulted lower than 5%, and no significant bias were observed at 95% of statistical confidence. Satisfactory prediction for CDs concentration was obtained with recovery values between 80.0-115%. Additional supporting information may be found online in the Supporting Information section at the end of the article. Color online: See article online to view Figs. 1-4 in color. This article is protected by copyright. All rights reserved.

PMID:35041772 | DOI:10.1002/elps.202100233

Br J Dermatol. 2022 Jan 18. doi: 10.1111/bjd.21020. Online ahead of print.

ABSTRACT

BACKGROUND: People with psoriasis can experience psychological distress that might be amenable to psychosocial self-help.

OBJECTIVES: This study tested the feasibility and acceptability of two theoretically developed self-help interventions designed to reduce feelings of shame and improve quality of life.

METHODS: A randomised controlled feasibility trial was conducted with one hundred and thirty participants with psoriasis who were randomly allocated to receive either compassion-based self-help (n =65) or mindfulness-based self-help (n =65), over a four-week period.

RESULTS: The interventions were found to be acceptable with over 70% of study completers reported finding the materials helpful. Ninety-two participants completed the study with attrition at 30%. Both interventions showed modest yet statistically significant reductions in shame (d = .20) and improvements in quality of life (d = .40).

CONCLUSIONS: Self-help based on compassion and mindfulness is acceptable to users and can reduce feelings of shame and improve quality of life for people living with psoriasis.

PMID:35041766 | DOI:10.1111/bjd.21020