Miracle-dz/UniFAR-FTUs huggingface dataset:
UHPLC‐ESI‐QTOF‐MS/MS Based Identification, Quantification, and Assessment of in Silico Molecular Interactions of Major Phytochemicals from Bioactive Fractions of Clerodendrum glandulosum Lindl. Leaves

Clerodendrum glandulosum Lindl. , is an ethnopharmacologically important species of the North‐eastern region of India. Leaves of this plant are consumed as food and traditionally used as medicine to cure hypertension, diabetes, and other metabolic syndromes. This study was designed to explore the antioxidant potential in the Clerodendrum leaves guided by in‐vitro activity, which is responsible for the therapeutic benefits. Leaves were extracted with 95 % methanol and further fractionated with solvents of varying polarities (e. g., petroleum ether, ethyl acetate, and butanol). Total phenolic and total flavonoid content of the crude extract/ fractions were measured by Folin‐Ciocalteu and AlCl3 methods, respectively. Crude extract/ fractions were screen for in‐vitro antioxidant and cytoprotective activities to determine the most bioactive fraction. Simultaneously, the chemical constituents of these fractions were identified and characterized using UHPLC‐ESI‐QTOF‐MS/MS. Subsequently, major phenolic compounds identified were subjected to in‐silico molecular docking with pro‐oxidant enzymes to elucidate possible biological functions. Both ethyl acetate and butanol fractions showed the presence of a high concentration of phenolic and flavonoid content along with the best antioxidant and cytoprotective properties compared to all other fractions. Chemical profiling of these active fractions revealed the presence of different phenolic compounds, among which verbascoside was the principal compound. These major phytoconstituents also exhibited strong binding interactions with the crucial amino acid residues of the target proteins, which complemented the in‐vitro bioactivities. In conclusion, this study offers structured information on antioxidant phytochemicals present in C. glandulosum leaves, which would be worthwhile for future investigations on the therapeutic properties at the molecular level.
The role of working memory loads on immediate and long-term sentence recall

ABSTRACT It is well-established that both phonological and semantic knowledge influence verbal working memory. However, the focus has primarily been on understanding phonological effects despite evidence of semantic influences. Articulatory suppression is a well-established task for preventing phonological processing. Methods to prevent semantic processing have rarely been used in the past, highlighting a need for developing a semantic interference task. We, therefore, conceptualised two novel tasks – an animacy categorisation and semantic relatedness judgement task. This study explored the impact of phonological (articulatory suppression) and semantic loads (animacy categorisation and semantic relatedness judgement) on immediate and delayed sentence recall. Additionally, sentence concreteness (concrete vs. abstract sentences) indexed semantic knowledge in verbal working memory. Across two studies, immediate recall revealed that articulatory suppression (preventing phonological processing) increased the size of the concreteness effect, while the novel semantic tasks (preventing semantic processing) reduced it suggesting that our semantic tasks were indeed imposing a semantic load. Further, relative long-term performance showed that more new words were remembered in articulatory suppression, whereas recall was disproportionately impaired in the semantic relatedness task. Our experimental paradigm offers phonological and semantic suppression tasks that can be used in parallel to investigate the interactions between working memory and language.
A scoping review on the health effects of smoke haze from vegetation and peatland fires in Southeast Asia: Issues with study approaches and interpretation

Smoke haze due to vegetation and peatland fires in Southeast Asia is a serious public health concern. Several approaches have been applied in previous studies; however, the concepts and interpretations of these approaches are poorly understood. In this scoping review, we addressed issues related to the application of epidemiology (EPI), health burden estimation (HBE), and health risk assessment (HRA) approaches, and discussed the interpretation of findings, and current research gaps. Most studies reported an air quality index exceeding the ‘unhealthy’ level, especially during smoke haze periods. Although smoke haze is a regional issue in Southeast Asia, studies on its related health effects have only been reported from several countries in the region. Each approach revealed increased health effects in a distinct manner: EPI studies reported excess mortality and morbidity during smoke haze compared to non-smoke haze periods; HBE studies estimated approximately 100,000 deaths attributable to smoke haze in the entire Southeast Asia considering all-cause mortality and all age groups, which ranged from 1,064–260,000 for specified mortality cause, age group, study area, and study period; HRA studies quantified potential lifetime cancer and non-cancer risks due to exposure to smoke-related chemicals. Currently, there is a lack of interconnection between these three approaches. The EPI approach requires extensive effort to investigate lifetime health effects, whereas the HRA approach needs to clarify the assumptions in exposure assessments to estimate lifetime health risks. The HBE approach allows the presentation of health impact in different scenarios, however, the risk functions used are derived from EPI studies from other regions. Two recent studies applied a combination of the EPI and HBE approaches to address uncertainty issues due to the selection of risk functions. In conclusion, all approaches revealed potential health risks due to smoke haze. Nonetheless, future studies should consider comparable exposure assessments to allow the integration of the three approaches.
Transcription and splicing regulation by NLRC5 shape the interferon response in human pancreatic β cells

IFNα is a key regulator of the dialogue between pancreatic β cells and the immune system in early type 1 diabetes (T1D). IFNα up-regulates HLA class I expression in human β cells, fostering autoantigen presentation to the immune system. We observed by bulk and single-cell RNA sequencing that exposure of human induced pluripotent-derived islet-like cells to IFNα induces expression of HLA class I and of other genes involved in antigen presentation, including the transcriptional activator NLRC5. We next evaluated the global role of NLRC5 in human insulin-producing EndoC-βH1 and human islet cells by RNA sequencing and targeted gene/protein determination. NLRC5 regulates expression of HLA class I, antigen presentation–related genes, and chemokines. NLRC5 also mediates the effects of IFNα on alternative splicing, a generator of β cell neoantigens, suggesting that it is a central player of the effects of IFNα on β cells that contribute to trigger and amplify autoimmunity in T1D.
Clinical features of pediatric IgA Vasculitis patients with scrotal involvement.

OBJECTIVES Immunoglobulin (Ig) A vasculitis (IgAV), the most common vasculitis of childhood. Scrotal involvement is relatively rare. In this study, we aimed to reveal the clinical and laboratory characteristics of patients with scrotal involvement in IgAV and its relationship with other clinical features of the disease. METHODS A total number of 301 male patients with a diagnosis of IgAV between January 2005-2022 were retrospectively analyzed. The patients were divided into two groups as with and without scrotal involvement. The clinical and laboratory characteristics of the groups were compared. RESULTS Scrotal involvement was detected in 16.3% (49) of male IgAV patients. Scrotal involvement was unilateral in 51% of patients. While single acute scrotal attack was present in 93.9% of patients, only 3 patients had recurrent acute scrotal involvement. In patients with scrotal involvement, the age at diagnosis was younger (p = 0.007) and disease recurrence was higher (p = 0.003). Glucocorticoid use was more common in patients with scrotal involvement (p < 0.001). In multivariable analysis, a statistically significant relation between scrotal involvement and age at diagnosis (OR = 0.85,95% CI0.76-0.96 p = 0.006) was detected. CONCLUSIONS In IgAV patients with scrotal involvement, the age at diagnosis is lower, steroid use is more common, and recurrent disease is more frequent.
A COMPUTER PROGRAM FOR PHYSICAL-OPTICS SCATTERING BY CONVEX CONDUCTING TARGETS

Abstract : This report describes a digital computer program which uses the physical optics approximation to calculate the scattering properties of convex perfectly conducting targets with arbitrary shape. The target shape is described in terms of the coordinates of a large number of points on the surface. The program handles bistatic as well as backscattering problems. The input data specify the frequency, the incidence angles and the scattering angles. In the CW case, the output data give the complex elements in the scattering matrix. The program also handles the pulse case where the incident waveform has a finite number of cycles. Graphs are included to illustrate typical results for the following target shapes: sphere, spheroids, ogive, and cone.
Clinical and programmatic outcomes of HIV-exposed infants enrolled in care at geographically diverse clinics, 1997–2021: A cohort study

Background Although 1·3 million women with HIV give birth annually, care and outcomes for HIV-exposed infants remain incompletely understood. We analyzed programmatic and health indicators in a large, multidecade global dataset of linked mother–infant records from clinics and programs associated with the International epidemiology Databases to Evaluate AIDS (IeDEA) consortium. Methods and findings HIV-exposed infants were eligible for this retrospective cohort analysis if enrolled at <18 months at 198 clinics in 10 countries across 5 IeDEA regions: East Africa (EA), Central Africa (CA), West Africa (WA), Southern Africa (SA), and the Caribbean, Central, and South America network (CCASAnet). We estimated cumulative incidences of DNA PCR testing, loss to follow-up (LTFU), HIV diagnosis, and death through 24 months of age using proportional subdistribution hazard models accounting for competing risks. Competing risks were transfer, care withdrawal, and confirmation of negative HIV status, along with LTFU and death, when not the outcome of interest. In CA and EA, we quantified associations between maternal/infant characteristics and each outcome. A total of 82,067 infants (47,300 EA, 10,699 CA, 6,503 WA, 15,770 SA, 1,795 CCASAnet) born from 1997 to 2021 were included. Maternal antiretroviral therapy (ART) use during pregnancy ranged from 65·6% (CCASAnet) to 89·5% (EA), with improvements in all regions over time. Twenty-four-month cumulative incidences varied widely across regions, ranging from 12·3% (95% confidence limit [CL], 11·2%,13·5%) in WA to 94·8% (95% CL, 94·6%,95·1%) in EA for DNA PCR testing; 56·2% (95% CL, 55·2%,57·1%) in EA to 98·5% (95% CL, 98·3%,98·7%) in WA for LTFU; 1·9% (95% CL, 1·6%,2·3%) in WA to 10·3% (95% CL, 9·7%,10·9%) in EA for HIV diagnosis; and 0·5% (95% CL, 0·2%,1·0%) in CCASAnet to 4·7% (95% CL, 4·4%,5·0%) in EA for death. Although infant retention did not improve, HIV diagnosis and death decreased over time, and in EA, the cumulative incidence of HIV diagnosis decreased substantially, declining to 2·9% (95% CL, 1·5%,5·4%) in 2020. Maternal ART was associated with decreased infant mortality (subdistribution hazard ratio [sdHR], 0·65; 95% CL, 0·47,0·91 in EA, and sdHR, 0·51; 95% CL, 0·36,0·74 in CA) and HIV diagnosis (sdHR, 0·40; 95% CL, 0·31,0·50 in EA, and sdHR, 0·41; 95% CL, 0·31,0·54 in CA). Study limitations include potential misclassification of outcomes in real-world service delivery data and possible nonrepresentativeness of IeDEA sites and the population of HIV-exposed infants they serve. Conclusions While there was marked regional and temporal heterogeneity in clinical and programmatic outcomes, infant LTFU was high across all regions and time periods. Further efforts are needed to keep HIV-exposed infants in care to receive essential services to reduce HIV infection and mortality.
The Role of Structural Order in the Mechanism of Charge Transport across Tunnel Junctions with Various Iron-Storing Proteins.

In biomolecular electronics, the role of structural order in charge transport (CT) is poorly understood. It has been reported that the metal oxide cores of protein cages (e.g., iron oxide and ferrihydrite nanoparticles (NPs) present in ferritin and E2-LFtn, which is E2 protein engineered with an iron-binding sequence) play an important role in the mechanism of CT. At the same time, the NP core also plays a major role in the structural integrity of the proteins. This paper describes the role of structural order in CT across tunnel junctions by comparing three iron-storing proteins. They are (1) DNA binding protein from starved cells (Dps, diameter (∅) = 9 nm); (2) engineered archaeal ferritin (AfFtn-AA, ∅ = 12 nm); and (3) engineered E2 of pyruvate dehydrogenase enzyme complex (E2-LFtn, ∅ = 25 nm). Both holo-Dps and apo-Dps proteins undergo CT by coherent tunneling because their globular architecture and relative structural stability provide a coherent conduction pathway. In contrast, apo-AfFtn-AA forms a disordered structure across which charges have to tunnel incoherently, but holo-AfFtn-AA retains its globular structure and supports coherent tunneling. The large E2-LFtn always forms disordered structures across which charges incoherently tunnel regardless of the presence of the NP core. These findings highlight the importance of structural order in the mechanism of CT across biomolecular tunnel junctions.
Using transverse optical patterns for ultra-low-light all-optical switching

Abstract : All-optical devices allow improvements in the speed of optical communication and computation systems by avoiding the conversion between the optical and electronic domains. The focus of this thesis is the experimental investigation of a new type of all-optical switch that is based on the control of optical patterns formed by nonlinear interactions between light and matter. The all-optical switch consists of a pair of light beams that counter propagate through warm rubidium vapor. These beams induce a nonlinear optical instability that gives rise to mirrorless parametric self-oscillation and generates light in the state of polarization that is orthogonal to that of the pump beams. In the far-field, the generated light forms patterns consisting of two or more spots. To characterize this instability I observe experimentally the amount of generated power and the properties of the generated patterns as a function of pump beam intensity, frequency, and size. Near an atomic resonance, the instability has a very low threshold: with less than 1 mW of total pump power, greater than 3 microwatts of power is generated. To apply this system to all-optical switching, I observe that the orientation of the generated patterns can be controlled by introducing a symmetry-breaking perturbation to the system. A perturbation in the form of a weak switch beam injected into the nonlinear medium is suitable for controlling the orientation of the generated patterns. The device operates as a switch where each state of the pattern orientation corresponds to a state of the switch, and spatial filtering of the generated pattern defines the output ports of the device. Measurements of the switch response show that it can be actuated by as few as 600 plus or minus 40 photons.
Presence and clinical significance of acellular mucin pools in resected rectal cancer with pathological complete response after pre‐operative chemoradiotherapy

For patients with locally advanced rectal cancer (LARC), a pathological complete response (pCR) after pre‐operative chemoradiotherapy (CRT) does not necessarily indicate a cure. Acellular mucin pools are often seen in patients with pCR. However, the clinical significance of acellular mucin pools in this group of patients remains unknown. This was a retrospective analysis of 225 LARC patients who achieved pCR following CRT and total mesorectal resection from 2011 to 2018. The outcomes of 5‐year disease‐free survival (DFS), 5‐year overall survival (OS) and 5‐year distant metastasis‐free survival (DMFS) were compared in patients with versus without acellular mucin pools. Among 225 pCR patients, acellular mucin pools could be identified in 56 (24.9%) patients, and recurrence occurred in 30 (13.3%) patients at 5 years. Distant recurrence was seen in 13 (23.2%) patients with acellular mucin pools and in 17 (10.1%) patients without acellular mucin pools. Patients with acellular mucin pools versus those without had poorer DFS (76.8 versus 89.9%, P = 0.010) and OS (87.5 versus 97.0%, P = 0.004) at 5 years. The presence of acellular mucin pools was the independent parameter that remained significant for DFS [hazard ratio (HR) = 3.904; 95% confidence interval (CI) = 1.342–11.356; P = 0.047] and OS (HR = 3.850; 95% CI = 1.214–12.213; P = 0.022) on multivariate analysis. A total of 17 patients demonstrated acellular mucin pools in primary tumour and lymph nodes. Subgroup analysis demonstrated that pCR patients with acellular mucin pools in primary tumour and lymph nodes were more likely to develop distant metastasis compared to pCR patients with acellular mucin pools only in primary tumour (47.1 versus 12.8%, P = 0.005). In summary, acellular mucin pools in LARC patients with pCR after CRT might represent a sign of invasive tumour biology and significantly shorten the prognosis of patients, especially in patients with acellular mucin pools in lymph nodes.
Learning, Large Scale Inference, and Temporal Modeling of Determinantal Point Processes

Determinantal Point Processes (DPPs) are random point processes well-suited for modelling repulsion. In discrete settings, DPPs are a natural model for subset selection problems where diversity is desired. For example, they can be used to select relevant but diverse sets of text or image search results. Among many remarkable properties, they offer tractable algorithms for exact inference, including computing marginals, computing certain conditional probabilities, and sampling. In this thesis, we provide four main contributions that enable DPPs to be used in more general settings. First, we develop algorithms to sample from approximate discrete DPPs in settings where we need to select a diverse subset from a large amount of items. Second, we extend this idea to continuous spaces where we develop approximate algorithms to sample from continuous DPPs, yielding a method to select point configurations that tend to be overly-dispersed. Our third contribution is in developing robust algorithms to learn the parameters of the DPP kernels, which is previously thought to be a difficult, open problem. Finally, we develop a temporal extension for discrete DPPs, where we model sequences of subsets that are not only marginally diverse but also diverse across time. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Statistics First Advisor Eric T. Bradlow
Private Stochastic Optimization in the Presence of Outliers: Optimal Rates for (Non-Smooth) Convex Losses and Extension to Non-Convex Losses

We study diﬀerentially private (DP) stochastic optimization (SO) with data containing outliers and loss functions that are not Lipschitz continuous. To date, the vast majority of work on DP SO assumes that the loss is Lipschitz (i.e. stochastic gradients are uniformly bounded), and their error bounds scale with the Lipschitz parameter of the loss. While this assumption is convenient, it is often unrealistic: in many practical problems where privacy is required, data may contain outliers and/or be unbounded, causing some stochastic gradients to have large norm. In such cases, the Lipschitz parameter may be prohibitively large, leading to vacuous excess risk bounds. Thus, building on a recent line of work [WXDX20, KLZ22], we make the weaker assumption that stochastic gradients have bounded k -th moments for some k ě 2 . Compared with works on DP Lipschitz SO, our excess risk scales with the k -th moment bound instead of the Lipschitz parameter of the loss, allowing for signiﬁcantly faster rates in the presence of outliers. For convex and strongly convex loss functions, we provide the ﬁrst asymptotically optimal excess risk bounds (up to a logarithmic factor). Moreover, in contrast to the prior works [WXDX20, KLZ22], our bounds do not require the loss function to be diﬀerentiable/smooth. We also devise an accelerated algorithm that runs in linear time and yields improved (compared to prior works) and nearly optimal excess risk for smooth losses. Additionally, our work is the ﬁrst to address non-convex non-Lipschitz loss functions satisfying the Proximal-PL inequality ; this covers some classes of neural nets, among other practical models. Our Proximal-PL algorithm has nearly optimal excess risk that almost matches the strongly convex lower bound. Lastly, we provide shuﬄe DP variations of our algorithms, which do not require a trusted curator (e.g. for distributed learning).
FFPA-Net: Efficient Feature Fusion with Projection Awareness for 3D Object Detection

Promising complementarity exists between the texture features of color images and the geometric information of LiDAR point clouds. However, there still present many challenges for efficient and robust feature fusion in the field of 3D object detection. In this paper, first, unstructured 3D point clouds are filled in the 2D plane and 3D point cloud features are extracted faster using projection-aware convolution layers. Further, the corresponding indexes between different sensor signals are established in advance in the data preprocessing, which enables faster cross-modal feature fusion. To address LiDAR points and image pixels misalignment problems, two new plug-and-play fusion modules, LiCamFuse and BiLiCamFuse, are proposed. In LiCamFuse, soft query weights with perceiving the Euclidean distance of bimodal features are proposed. In BiLiCamFuse, the fusion module with dual attention is proposed to deeply correlate the geometric and textural features of the scene. The quantitative results on the KITTI dataset demonstrate that the proposed method achieves better feature-level fusion. In addition, the proposed network shows a shorter running time compared to existing methods.