Miracle-dz/UniFAR-FTUs huggingface dataset:
Advances of Single-Cell Protein Analysis

Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.
Home-based rehabilitation using smart wearable knee exercise device with electrical stimulation after anterior cruciate ligament reconstruction

Abstract Introduction: Rehabilitation after anterior cruciate ligament (ACL) reconstruction is critical to patient outcome. Despite its importance; however, hospital-based rehabilitation is limited, with barriers, including distance and cost. With recent technological advancements, wearable devices have actively been used to address these barriers. In this study, we propose a randomized controlled trial protocol investigating the efficacy and feasibility of home-based rehabilitation after ACL reconstruction using a smart wearable device providing electrical stimulation that allows knee exercise. Methods and analysis: This is a protocol proposal for a prospective, single-center, randomized, controlled study. We plan to recruit adults discharged after ACL reconstruction; the recruited subjects will be randomly allocated to 1 of 2 groups, using a computer-generated randomization method: the intervention (n = 20) or control group (n = 20). The intervention group will receive a 6-week home-based rehabilitation program using smart wearable device. The control group will undergo a 6-week self-exercise program as normal. The following outcomes will be assessed at baseline, 2 weeks, and 6 weeks post the 6-week intervention program: quadriceps strength of the affect side as measured by a dynamometer (primary outcome); range of motion; root mean square of quadriceps muscle using surface electromyography; knee function using questionnaire; quality of life; subject's satisfaction score using questionnaire; frequency and duration of exercise; and knee pain. An intention-to-treat analysis will be conducted for the primary outcome. Discussion: This study is a prospective, single-center, randomized, controlled study. This study aims to research the feasibility and efficacy of a 6-week, structured home-based rehabilitation program for patients after ACL reconstruction using a smart wearable device. The findings of this study will help to establish a home-based rehabilitation program to better recovery in patients with ACL reconstruction. Trial registration number: This protocol was registered in ClinicalTrials.gov, under the number NCT04079205.
Transcriptomic Evidence of Molecular Mechanisms Underlying the Response of Lactobacillus plantarum WCFS1 to Hydroxytyrosol

This study was aimed to gain new insights into the molecular mechanisms used by Lactobacillus plantarum WCFS1 to respond to hydroxytyrosol (HXT), one of the main and health-relevant plant phenolics present in olive oil. To this goal, whole genome transcriptomic profiling was used to better understand the contribution of differential gene expression in the adaptation to HXT by this microorganism. The transcriptomic profile reveals an HXT-triggered antioxidant response involving genes from the ROS (reactive oxygen species) resistome of L. plantarum, genes coding for H2S-producing enzymes and genes involved in the response to thiol-specific oxidative stress. The expression of a set of genes involved in cell wall biogenesis was also upregulated, indicating that this subcellular compartment was a target of HXT. The expression of several MFS (major facilitator superfamily) efflux systems and ABC-transporters was differentially affected by HXT, probably to control its transport across the membrane. L. plantarum transcriptionally reprogrammed nitrogen metabolism and involved the stringent response (SR) to adapt to HXT, as indicated by the reduced expression of genes involved in cell proliferation or related to the metabolism of (p)ppGpp, the molecule that triggers the SR. Our data have identified, at genome scale, the antimicrobial mechanisms of HXT action as well as molecular mechanisms that potentially enable L. plantarum to cope with the effects of this phenolic compound.
Retention of the Enzymatic Activity and Product Properties During Spray Drying of Pineapple Stem Extract in Presence of Maltodextrin

The aim of this work was to investigate the effects of drying parameters on the retention of the enzymatic activity and on the physical properties of spray-dried pineapple stem extract. A Box and Behnken experimental design was used to investigate the effects of the processing parameters on the product properties. The parameters studied were the inlet temperature of drying gas (Tgi), the feed flow rate of the pineapple extract relative to evaporative capacity of the system (Ws /Wmax), and the concentration of maltodextrin added to the extract (MD). Significant effects of the processing parameters on the retention of the proteolytic activity of the powdered extract were observed. High processing temperatures lead to a product with a smaller moisture content, particle size, and lower agglomerating tendency. A product with insignificant losses of the proteolytic activity (≈ 10%) and low moisture content (less than 6.5%) is obtained at selected conditions.
Macronutrient-Use Efficiency and Changes in Chemical Properties of an Oxisol as Influenced by Phosphorus Fertilization and Tropical Cover Crops

Cover crops are important components of copping systems due to their beneficial effects on soil physical, chemical, and biological properties. A greenhouse experiment was conducted to evaluate influence of phosphorus (P) fertilization on nutrient-use efficiency of 14 tropical cover crops. The P levels tested were 0 (low), 100 (medium), and 200 (high) mg kg−1 of soil. The cover crops tested were Crotalaria breviflora, Crotalaria breviflora, Crotalaria spectabilis Roth, Crotalaria ochroleuca G. Don, Crotalaria juncea L. , Crotalaria mucronata, Calapogonium mucunoides, Pueraria phaseoloides Roxb. , Pueraria phaseoloides Roxb. , Cajanus cajan L. Millspaugh, Dolichos lablab L. , Mucuna deeringiana (Bort) Merr. , Mucuna cinereum L. , and Canavalia ensiformis L. DC. Agronomic efficiency (shoot dry weight per unit P applied), physiological efficiency (shoot dry weight per unit of nutrient uptake), and apparent recovery efficiency (nutrient uptake in the shoot per unit nutrient applied) were significantly varied among cover crops. Agronomic efficiency decreased with increasing P levels. Overall, physiological efficiency of nutrient uptake was in the order of P > sulfur (S) > magnesium (Mg) > calcium (Ca) > potassium (K) > nitrogen (N). Similarly, apparent recovery efficiency was in the order of N > K > Ca > Mg > P > S. Different recovery efficiency in cover crops can be useful in selecting cover crops with high recovery efficiency, which may be beneficial to succeeding crops in the cropping systems. The P × cover crops interactions were significant for soil extractable Ca2+, P, cation exchange capacity (CEC), Ca saturation, Ca/K ratio, and K/Mg ratio, indicating that cover crops change these soil property differently under different P levels. Thus, cover crops selection for different P levels is an important strategy for using cover crops in cropping systems in Brazilian Oxisols. Optimal values of soil pH, soil Ca and Mg contents, hydrogen (H) + aluminum (Al), P, CEC, base saturation, Ca saturation, Mg saturation, and K saturation were established for tropical cover crops grown on an Oxisol.
Outcomes in Advanced Stage Epithelial Ovarian, Fallopian Tubal, and Peritoneal Cancer after Primary Surgery and Adjuvant Chemotherapies: A Single-Institute Real-World Experience

Debulking surgery followed by systemic chemotherapy—including three-weekly intravenous paclitaxel and carboplatin (GOG-158)—is the cornerstone for advanced epithelial ovarian, fallopian tubal, and peritoneal cancer (EOC) treatment. In this scenario, Federation of Gynecology and Obstetrics (FIGO) stage, cell types, completeness of surgery, lymph nodes (LN) status, adjuvant chemotherapy regimens, survival status, progression-free survival (PFS), and overall survival (OS) of 192 patients diagnosed as having stage IIIA1–IVB EOC over January 2008–December 2017 were analyzed retrospectively. Of them, 100 (52.1%) patients had been debulked optimally. Of all cases, 64.1% and 10.9% demonstrated serous and clear-cell carcinoma. Moreover, the FIGO stage, surgery completeness, and LN status affected recurrence/persistence and mortality (all p < 0.001). Clear cell carcinoma led to shorter survival than serous carcinoma (p = 0.002). Adjuvant chemotherapy regimens were divided into five main groups according to previous clinical trials. However, choice of chemotherapy failed to demonstrate significant differences in patient outcomes. Similar results were found in the sub-analysis of optimally debulked cases, except that intraperitoneal chemotherapy could reduce mortality risk when compared with GOG-158 (p = 0.042). Notably, retroperitoneal LN dissection in all cases or optimally debulked cases reduced risks of recurrence/persistence and mortality, and prolonged PFS and OS significantly (all p < 0.05). Without optimal debulking, LN dissection led to little improvement in outcomes. Various modified chemotherapy regimens did not prolong PFS and OS or reduce recurrence/persistence and mortality risks. LN dissection is strongly recommended to improve the completeness of surgery and patient outcome. Clear cell type has a poorer outcome than serous type, which requires more aggressive treatment and follow-up.
Severe epithelial dysplasia of the fallopian tube: a potential source of malignancy arising from an often ignored organ

Case report A 49-year-old woman, was seen in the gynaecology out-patients clinic complaining of left-sided abdominal discomfort. She had a family history of bowel and ovarian cancer. Her mother and maternal grandmother both had bowel cancer, the former at the age of 71 and the latter at the age of 66. Her sister had died at the age of 53 from ovarian cancer. On examination of her family tree, it was indicated that cancer was inherited in this family. Looking at the inheritance pattern, it would be the hereditary non-polyposis colorectal cancer, Lynch type II in which colorectal cancer is inherited with other epithelial cancers, particularly ovarian and uterine. This condition is inherited as an autosomal dominant trait, in which case she would be at risk of both colorectal and ovarian cancer. An ultrasound scan examination of her pelvis and a colonoscopic screening proved negative. However, in view of the strong family history, the patient requested a bilateral oophorectomy as a prophylactic measure but did not wish a total abdominal hysterectomy to be carried out at the same time. At laparatomy, both ovaries and parts of the fallopian tubes were removed, omental and peritoneal biopsies were also obtained. The patient made an uneventful recovery and was discharged from the hospital 4 days after the operation. The histology report on the specimens con® rmed normal ovaries with no evidence of malignancy. The histology of both fallopian tubes, however, showed multifocal, severe dysplasia. It was also reported that as the tubes were not removed in their entirety complete excision of the lesion could not be con® rmed. Hence, a second laparatomy was carried out to remove the tubal remnants, the uterus as well as omental and additional peritoneal biopsies. The histology report on the specimens showed no evidence of abnormality in either fallopian tube. The myometrium contained multiple ® broids and the endometrium was menopausal. The cervix was normal as were the peritoneal biopsies. There was no evidence of malignancy in any of the other specimens removed.
Muscle mass assessed by D3-Creatine dilution method and incident self-reported disability and mortality in a prospective observational study of community dwelling older men.

BACKGROUND Whether low muscle mass is a risk factor for disability and mortality is unclear. Associations between approximations of muscle mass (including lean mass from dual energy x-ray absorptiometry (DXA)) and these outcomes are inconsistent. METHODS Muscle mass measured by deuterated creatine (D3Cr) dilution and appendicular lean mass (ALM, by DXA) were assessed at the Year 14 Visit (2014-6) of the prospective MrOS study (N=1425, age 77-101 years). Disability in activities of daily living (ADLs), instrumental ADLS (IADLs), and mobility tasks was self-reported at the Year 14 visit and 2.2 years later; deaths were centrally adjudicated over 3.3 years. Relative risks (RR) and 95% confidence intervals (CI) were estimated per standard deviation decrement with negative binomial, logistic regression or proportional hazards models. RESULTS In age and clinical center adjusted models, the RR per decrement in D3Cr muscle mass/wgt was 1.9 (95% CI: 1.2, 3.1) for incident self-reported ADL disability; 1.5 (95% CI: 1.3, 1.9) for IADL disability; and 1.8 (95% CI: 1.5, 2.2) for mobility disability. In age, clinical center and weight adjusted models, the RR per decrement in D3Cr muscle mass was 1.8 (95% CI: 1.5, 2.2) for all-cause mortality. In contrast, lower DXA ALM was not associated with any outcome. Associations of D3Cr muscle mass with these outcomes were slightly attenuated after adjustment for confounding factors and the potentially mediating effects of strength and physical performance. CONCLUSIONS Low muscle mass as measured by D3Cr dilution is a novel risk factor for clinically meaningful outcomes in older men.
Letter to the Editor

Recently, we read a paper by Mimura et al entitled ‘Hearing loss in patients with enlarged vestibular aqueduct: Air-bone gap and audiological Bing test’ that was published in your Journal (Mimura et al, 2005). The authors speculated on the origin of the air-bone gap that is often found in patients with enlarged vestibular aqueduct. In their discussion they drew a parallel with similar observations reported in patients with enlarged internal auditory canal (so-called stapes gusher patients). The authors argued that the air-bone gap in their patients was probably not due to middle ear problems but rather an artefact of boneconduction testing. The abnormal ‘third cochlear window’ is thought to play a disturbing role, resulting in bone-conduction thresholds that are not correct. This hypothesis is not new, as it was already published in 1995 (Snik et al, 1995). We studied patients with an enlarged internal auditory canal, using a set of auditory tests, and we showed that although an air-bone gap was found, the patients suffered from sensorineural hearing loss. The explanation that we gave was the same as that described in the paper of Mimura et al; obviously, our paper escaped the authors’ notice. Papers on pitfalls in audiometric testing remain of high importance because such pitfalls might lead to erroneous diagnosis and treatment. I think that Mimura and co-workers will agree with us that cross-validation in audiometry remains of prime importance. As indicated in our paper, the use of a proper set of standard audiometric tests might avoid misdiagnosis in such patients. The Bing test, as reintroduced by Mimura et al (2005) might be a valuable addition.
Development and Preliminary Validation of the Couples’ Stigma Scale to Assess Self-Stigma among the Partners of Persons with Autism Spectrum Disorder in Japan

Spouses of individuals with autism spectrum disorder (ASD) may struggle with self-stigma and may require attention and care; however, no scale exists to measure the stigma of spouses of persons with ASD. This study created and investigated the construct validity of the Couples Stigma Scale. This scale consists of 14 items and it was designed based on prior literature, interviews, and the self-stigma theory to assess the self-stigma experienced by spouses of people with ASD. A survey was conducted with spouses of persons with ASD who participated in a self-help group. Responses were obtained from 259 people, of which 253 women were included in the analysis. Exploratory factor analysis was performed separately with two independent groups, indicating a four-factor structure, to determine structural validity. The factor loadings of the items constituting the four factors were 0.39 or greater. Regarding external validity, the correlation coefficient between the Couples Stigma Scale and the World Health Organization Quality of Life (WHOQOL) score was −0.341 (p < 0.001), and the domain correlation coefficient was significant for all relevant WHOQOL domains. Our results suggest that the Japanese version of the Couples Stigma Scale is a valid instrument for assessing self-stigma in the spouses of persons with ASD.
Important Role for Endothelins in Acute Hepatic Ischemia/Reperfusion Injury

The aim of this study was to explore the complex role of endothelins (ETs) in hepatic ischemia-reperfusion injury and to minimize this type of injury by nonselective ET receptor blockade. In an in vivo rat model, hepatic ischemia was induced for 30 min. The rats were divided into three groups: (1) sham operated, (2) untreated ischemic, and (3) group treated with the nonselective ET receptor antagonist bosentan (1 mg/kg body weight iv). Blockage of the ET system during ischemia-reperfusion was assessed by: (1) in vivo microscopic analysis, (2) measurement of local tissue pO2
Antibacterial Action of Nanoparticle Loaded Nanocomposites Based on Graphene and Its Derivatives: A Mini-Review

Bacterial infections constitute a severe problem in various areas of everyday life, causing pain and death, and adding enormous costs to healthcare worldwide. Besides, they cause important concerns in other industries, such as cloth, food packaging, and biomedicine, among others. Despite the intensive efforts of academics and researchers, there is lack of a general solutions to restrict bacterial growth. Among the various approaches, the use of antibacterial nanomaterials is a very promising way to fight the microorganisms due to their high specific surface area and intrinsic or chemically incorporated antibacterial action. Graphene, a 2D carbon-based ultra-thin biocompatible nanomaterial with excellent mechanical, thermal, and electrical properties, and its derivatives, graphene oxide (GO) and reduced graphene oxide (rGO), are highly suitable candidates for restricting microbial infections. However, the mechanisms of antimicrobial action, their cytotoxicity, and other issues remain unclear. This mini-review provides select examples on the leading advances in the development of antimicrobial nanocomposites incorporating inorganic nanoparticles and graphene or its derivatives, with the aim of providing a better understanding of the antibacterial properties of graphene-based nanomaterials.
High‐speed X‐ray‐induced luminescence computed tomography

X‐ray‐induced luminescence computed tomography (XLCT) is an emerging molecular imaging. Challenges in improving spatial resolution and reducing the scan time in a whole‐body field of view (FOV) still remain for practical in vivo applications. In this study, we present a novel XLCT technique capable of obtaining three‐dimensional (3D) images from a single snapshot. Specifically, a customed two‐planar‐mirror component is integrated into a cone beam XLCT imaging system to obtain multiple optical views of an object simultaneously. Furthermore, a compressive sensing based algorithm is adopted to improve the efficiency of 3D XLCT image reconstruction. Numerical simulations and experiments were conducted to validate the single snapshot X‐ray‐induced luminescence computed tomography (SS‐XLCT). The results show that the 3D distribution of the nanophosphor targets can be visualized much faster than conventional cone beam XLCT imaging method that was used in our comparisons while maintaining comparable spatial resolution as in conventional XLCT imaging. SS‐XLCT has the potential to harness the power of XLCT for rapid whole‐body in vivo molecular imaging of small animals.
Noise-Sensitive But More Precise Subcortical Representations Coexist with Robust Cortical Encoding of Natural Vocalizations

Humans and animals maintain accurate sound discrimination in the presence of loud sources of background noise. It is commonly assumed that this ability relies on the robustness of auditory cortex responses. However, only a few attempts have been made to characterize neural discrimination of communication sounds masked by noise at each stage of the auditory system and to quantify the noise effects on the neuronal discrimination in terms of alterations in amplitude modulations. Here, we measured neural discrimination between communication sounds masked by a vocalization-shaped stationary noise from multiunit responses recorded in the cochlear nucleus, inferior colliculus, auditory thalamus, and primary and secondary auditory cortex at several signal-to-noise ratios (SNRs) in anesthetized male or female guinea pigs. Masking noise decreased sound discrimination of neuronal populations in each auditory structure, but collicular and thalamic populations showed better performance than cortical populations at each SNR. In contrast, in each auditory structure, discrimination by neuronal populations was slightly decreased when tone-vocoded vocalizations were tested. These results shed new light on the specific contributions of subcortical structures to robust sound encoding, and suggest that the distortion of slow amplitude modulation cues conveyed by communication sounds is one of the factors constraining the neuronal discrimination in subcortical and cortical levels. SIGNIFICANCE STATEMENT Dissecting how auditory neurons discriminate communication sounds in noise is a major goal in auditory neuroscience. Robust sound coding in noise is often viewed as a specific property of cortical networks, although this remains to be demonstrated. Here, we tested the discrimination performance of neuronal populations at five levels of the auditory system in response to conspecific vocalizations masked by noise. In each acoustic condition, subcortical neurons better discriminated target vocalizations than cortical ones and in each structure, the reduction in discrimination performance was related to the reduction in slow amplitude modulation cues.