Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular Proximity Labeling Reveals an Expanded Interactome for the Matrisome Protein TIMP2

Classical methods of investigating protein-protein interactions (PPIs) are generally performed in non-living systems, yet in recent years new technologies utilizing proximity labeling (PL) have given researchers the tools to explore proximal PPIs in living systems. PL has distinct advantages over traditional protein interactome studies, such as the ability to identify weak and transient interactions in vitro and in vivo. Most PL studies are performed on targets within the cell or on the cell membrane. We have adapted the original PL method to investigate PPIs within the extracellular compartment, using both BioID2 and TurboID, that we term extracellular PL (ePL). To demonstrate the utility of this modified technique, we investigate the interactome of the widely expressed matrisome protein tissue inhibitor of metalloproteinases 2 (TIMP2). Tissue inhibitors of metalloproteinases (TIMPs) are a family of multi-functional proteins that were initially defined by their ability to inhibit the enzymatic activity of metalloproteinases (MPs), the major mediators of extracellular matrix (ECM) breakdown and turnover. TIMP2 exhibits a broad expression profile and is often abundant in both normal and diseased tissues. Understanding the functional transformation of matrisome regulators, like TIMP2, during the evolution of tissue microenvironments associated with disease progression is essential for the development of ECM-targeted therapeutics. Using carboxyl- and amino-terminal fusion proteins of TIMP2 with BioID2 and TurboID, we describe the TIMP2 proximal interactome. We also illustrate how the TIMP2 interactome changes in the presence of different stimuli, in different cell types, in unique culture conditions (2D vs 3D), and with different reaction kinetics (BioID2 vs. TurboID); demonstrating the power of this technique versus classical PPI methods. We propose that the screening of matrisome targets in disease models using ePL will reveal new therapeutic targets for further comprehensive studies.
Chemotaxis response and age-stage, two-sex life table of the Cheilomenes sexmaculata (Fabricius) (Coccinellidae: Coleoptera) against different aphid species

The Cheilomenes sexmaculata (Fabricius) (Coleoptera: Coccinellidae), is one of the most beneficial and identifiable predators of numerous soft-bodied and sucking insect pests of several crops. Biological parameters and olfactory response of C. sexmaculata were investigated under laboratory conditions by providing three different aphid species i.e., mustard aphid (Lipaphis erysimi Kaltenbach), citrus black aphid (Toxoptera citricida Kirkaldy), and peach aphid (Diuraphis noxia Kurdjumov) as a food source. The developmental period of immature stages of C. sexmaculata was shorter on D. noxia as compared to other aphid species. The adult longevities were longer on D. noxia and T. citricida while shorter on L. erysimi. Female fecundity was highest on D. noxia while lowest on L. erysimi. Life table parameters i.e., intrinsic rate of increase (r), finite rate of increase (λ), net reproductive rate (Ro), and gross reproductive rate (GRR) were maximum on D. noxia while minimum on L. erysimi. The mean generation time C. sexmaculata was 20.90, 23.69, and 26.2 days on D. noxia, L. erysimi, T. and citricida, respectively. These findings were further confirmed from the olfactory experiment where D. noxia proved to be the most preferred prey. This study provides necessary information for mass-rearing of C. sexmaculata.
The effects of N-acetylcysteine on hepatic, hematologic, and renal parameters in cirrhotic patients: a randomized controlled trial

Aim: To evaluate the effects of N-acetylcysteine (NAC) supplementation in cirrhotic patients. Background: Chronic hepatic inflammation leads to fibrosis and cirrhosis through various mechanisms such as oxidative stress. NAC is one of the intracellular precursors of glutathione that can degrade most reactive oxygen species. Recently, the beneficial effects of NAC in animal and human studies on preventing liver injury progression and improving liver function have been examined. However, more studies on human subjects are still required. Methods: Well-known cirrhotic patients with a specific etiology and aged 18 to 70 years who referred to the gastrointestinal clinic of Ayatollah Taleghani Hospital from December 2018 to December 2019 were enrolled in the present randomized double-blind controlled trial. Patients in the intervention group received NAC tablets at a dose of 600 mg daily, and the control group received a placebo. Demographic data, medical characteristics, and Child-Pugh and MELD scores evaluated at baseline and after 6 months. Results: Totally, 60 patients completed the present study (30 patients in the intervention group, and 30 patients in the control group). Hematological and biochemical parameters were normal in both groups with no significant differences at baseline and 6 months after intervention values. Moreover, the renal function indicators including serum creatinine (Cr) and urea (BUN) decreased significantly after intervention. Hepatic parameters also decreased significantly 6 months after intervention. Decreases in the renal and hepatic parameters 6 months after baseline in the control group were not statistically significant. Conclusion: The results of this study showed that NAC improved hepatic and renal function by decreasing serum urea and creatinine levels but had no significant effect on hematological and biochemical parameters. Furthermore, NAC significantly improved hepatic profiles by decreasing ALT, AST, and ALP in the liver enzymes between the intervention and control groups. Moreover, NAC caused a significant decrease in Child-Pugh and MELD scores.
Decrease in climatic conditions favouring floods in the south‐east of Belgium over 1959–2010 using the regional climate model MAR

The Ourthe River, in the south‐east of Belgium, has a catchment area of 3500 km2 and is one of the main tributaries of the Meuse River. In the Ourthe, most of the flood events (FE) occur during winter and about 50% of them are due to heavy rainfall events combined with an abrupt melting of the snowpack covering the Ardennes massif during winter. This study aims to determine whether trends in extreme hydroclimatic events generating floods can be detected over the last century in Belgium, where a global warming signal can be observed. Hydroclimatic conditions favourable to floods were reconstructed over 1959–2010 using the regional climate model MAR (‘Modèle Atmosphérique Régional’) forced by the ERA‐Interim/ERA‐40, the ERA‐20C and the NCEP/NCAR‐v1 reanalyses. Extreme run‐off events, which could potentially generate floods, were detected using run‐off caused by precipitation events and snowpack melting from the MAR model. In the validation process, the MAR‐driven temperature, precipitation and snow depth were successfully compared to daily weather data over the period 2008–2014 for 20 stations in Belgium. MAR also showed its ability to detect up to 90% of the hydroclimatic conditions which effectively generated observed floods in the Ourthe River over the period 1974–2010. Conditions favourable to floods in the Ourthe River catchment present a negative trend over the period 1959–2010 as a result of a decrease in snow accumulation and a shortening of the snow season. This trend is expected to accelerate in a warmer climate. However, regarding the impact of the extreme precipitation events evolution on conditions favouring floods, the signal is less clear because the trends depend on the reanalysis used to force the MAR model.
World Journal of Gastroenterology

Small nucleolar RNAs (snoRNAs) represent a class of non-coding RNAs that play pivotal roles in post-transcriptional RNA processing and modification, thereby contributing significantly to the maintenance of cellular functions related to protein synthesis. SnoRNAs have been discovered to possess the ability to influence cell fate and alter disease progression, holding immense potential in controlling human diseases. It is suggested that the dysregulation of snoRNAs in cancer exhibits differential expression across various cancer types, stages, metastasis, treatment response and/or prognosis in patients. On the other hand, colorectal cancer (CRC), a prevalent malignancy of the digestive system, is characterized by high incidence and mortality rates, ranking as the third most common cancer type. Recent research indicates that snoRNA dysregulation is associated with CRC, as snoRNA expression significantly differs between normal and cancerous conditions. Consequently, assessing snoRNA expression level and function holds promise for the prognosis and diagnosis of CRC. Nevertheless, current comprehension of the potential roles of snoRNAs in CRC remains limited. This review offers a comprehensive survey of the aberrant regulation of snoRNAs in CRC, providing valuable insights into the discovery of novel biomarkers, therapeutic targets, and potential tools for the diagnosis and treatment of CRC and furnishing critical cues for advancing research into CRC and the judicious selection of therapeutic targets
World Journal of Gastroenterology

Emerging evidence and perspectives have pointed towards the heart playing an important role in hepatorenal syndrome (HRS), outside of conventional understanding that liver cirrhosis is traditionally considered the sole origin of a cascade of pathophysiological mechanisms directly affecting the kidneys in this context. In the absence of established heart disease, cirrhotic cardiomyopathy may occur more frequently in those with liver cirrhosis and kidney disease. It is a specific form of cardiac dysfunction characterized by blunted contractile responsiveness to stress stimuli and altered diastolic relaxation with electrophysiological abnormalities. Despite the clinical description of these potential cardiac-related complications of the liver, the role of the heart has traditionally been an over-looked aspect of circulatory dysfunction in HRS. Yet from a physiological sense, temporality (prior onset) of cardiorenal interactions in HRS and positive effects stemming from portosystemic shunting demonstrated an important role of the heart in the development and progression of kidney dysfunction in cirrhotic patients. In this review, we discuss current concepts surrounding how the heart may influence the development and progression of HRS, and the role of systemic inflammation and endothelial dysfunction causing circulatory dysfunction within this setting. The temporality of heart and kidney dysfunction in HRS will be
World Journal of Gastroenterology

Colorectal cancer (CRC) screening is a fundamental tool in the prevention and early detection of one of the most prevalent and lethal cancers. Over the years, screening, particularly in those settings where it is well organized, has succeeded in reducing the incidence of colon and rectal cancer and improving the prognosis related to them. Despite considerable advancements in screening technologies and strategies, the effectiveness of CRC screening programs remains less than optimal. This paper examined the multifaceted reasons behind the persistent lack of effectiveness in CRC screening initiatives. Through a critical analysis of current methodologies, technological limitations, patient-related factors, and systemic challenges, we elucidated the complex interplay that hampers the successful reduction of CRC morbidity and mortality rates. While acknowledging the advancements that have improved aspects of screening, we emphasized the necessity of addressing the identified barriers comprehensively. This study aimed to raise awareness of how important CRC screening is in reducing costs for this disease. Screening and early diagnosis are not only important in improving the prognosis of patients with CRC but can lead to an important reduction in the cost of treating a disease that is often diagnosed at an advanced stage. Spending more sooner can mean saving money later.
Predicting fire behavior in palmetto-gallberry fuel complexes

--Rate of spread, fireline intensity, and flame length can be predicted with reasonable accuracy for backfires and lowintensity head fires in the palmetto-gallberry fuel complex of the South. This fuel complex was characterized and variables were adjusted for use in Rothermel's (1972) spread model. Age of rough, height of understory, percent of area covered by palmetto, basal area of overstory, season of year, moisture content of dead fuels, and midflame windspeed must be known to make predictions. These fire behavior predictions do not apply to high-intensity wildfires where spotting and crowning are occurring.
The impact of helophyte transpiration on vertical water exchange in water bodies

Abstract The article presents the results of experimental research on evapotranspiration and transpiration of a common reed bed. The study was conducted in 2014–2015 on Lake Raduńskie Górne (Kashubian Lakeland) in the summer half-year from 1 May to 31 October. In the experiment two sets of standard evaporimeters GGI-3000 were used. One of the evaporimeters was filled with water, while the second additionally contained common reed. During the experiment medium reed bed density was 240 shoots per square metre. The results of the study showed that during the research period the average daily common reed transpiration was 3.9 mm, and the daily maxima reached 12.1–12.5 mm. Average monthly transpiration totals ranged from 42.8 (October) to 208.5 mm (August). During the growing season, the loss of water to transpiration reached 872–971 mm. The average transpiration rate, determined in the conditions of already well developed reed bed (June-September), was 1.83 dm3 m−2 d−1. The values of the ratios Th/EO and ETh/EO, determined during the experiment, were within the ranges reported in most previous research. The average ratio Th/EO was 1.6, and the ratio ETh/EO was 2.0. These values indicate that during the vegetation period common reed transpiration is higher by 60% from open water evaporation, and the total water losses from the common reed bed to evapotranspiration are twice as high as water loss in open water evaporation.
Managing forest water quantity and quality under climate change

Water is a critical resource of the Southern United States and is intimately linked to other ecosystem and societal values. The South is known for its warm climate, rich water resources (Figure 9.1), and large acreage of forest lands that provide an ideal place for people to live. Indeed, water availability is central to sustaining an economy that relies on irrigation agriculture, forestry, recreation, 9
Role of wet-cupping therapy in physiological and mental pains in patients with migraine: A quasi-clinical trial

Background: There is growing evidence of the potential benefits of wet-cupping therapy in reducing physiological pain severity in migraine; however, the role of this therapy on mental pain is unclear in this process. Therefore, this study aimed to examine the effectiveness of wet-cupping therapy on physiological and mental pains in patients with migraine. In this study, 72 migraine patients were treated with wet-cupping therapy and followed up after 1 month. Methods: The severity of physiological and mental pain was measured before therapy, 10 minutes and 1 month following therapy. Results: The study showed that patients in the wet-cupping therapy had a significantly lower mean value of physiological (0.42 vs 3.39; P < .001) and mental pain (1.60 vs 3.06; P < .001) compared to the patients in the control group, respectively. The mean value of the physiological was significantly decreased from 6.97 (baseline) to 0.73 (10 minutes) and 0.63 (1 month; P < .001) in the wet-cupping therapy patients, and the mean value of mental pain from 3.76 (baseline) to 0.71 (10 minutes) and 1.71 (1 month; P < .001). The mean values of physiological and mental pains were significantly reduced (from 7.80–3.39; P < .001) and (from 3.48–3.06; P = .0044), respectively. The level of physiological pain severity was significantly decreased with a decreasing level of mental pain severity at the posttest within the control (r = 0.5471; P = .0002) and the wet-cupping therapy (r = 0.3814; P .0412). Conclusion: This study showed that the physiological pain was controlled by the mental pain in the wet-cupping therapy.
SARS-CoV-2 may play a direct role in the pathogenesis of posterior reversible encephalopathy syndrome (PRES) associated with COVID-19: A CARE-compliant case report and literature review

Rationale: During the past 3 years of the corona virus disease 2019 (COVID-19) pandemic, COVID-19 has been recognized to cause various neurological complications, including rare posterior reversible encephalopathy syndrome (PRES). In previously reported cases of PRES associated with COVID-19, the majority of patients had severe COVID-19 infection and known predisposing factors for PRES, such as uncontrolled hypertension, renal dysfunction, and use of immunosuppressants. It remains unclear whether these risk factors or infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to the development of PRES in these patients. Here we report a special case of PRES associated with COVID-19 without any known risk factors for PRES, indicating the SARS-CoV-2’s direct role in the pathogenesis of PRES associated with COVID-19. Patient concerns: An 18-year-old female patient presented to the emergency department with abdominal pain. Preliminary investigations showed no abnormalities, except for positive results in novel coronavirus nucleic acid tests using oropharyngeal swabs. However, the patient subsequently developed tonic–clonic seizures, headaches, and vomiting on the second day. Extensive investigations have been performed, including brain MRI and lumbar puncture. Brain MRI showed hypointense T1-weighted and hyperintense T2-weighted lesions in the bilateral occipital, frontal, and parietal cortices without enhancement effect. Blood and cerebrospinal fluid analyses yielded negative results. The patient had no hypertension, renal insufficiency, autoimmune disease, or the use of immunosuppressants or cytotoxic drugs. Diagnoses: PRES was diagnosed based on the clinical features and typical MRI findings of PRES. Interventions: Symptomatic treatments such as anticonvulsants were administered to the patients. Outcomes: The patient fully recovered within 1 week. The initial MRI abnormalities also disappeared completely on a second MR examination performed 11 days later, supporting the diagnosis of PRES. The patient was followed up for 6 months and remained in a normal state. Lessons: The current case had no classical risk factors for PRES, indicating that although the cause of PRES in COVID-19 patients may be multifactorial, the infection of SARS-CoV-2 may play a direct role in the pathogenesis of PRES associated with COVID-19.
Single cell measurements of bacterial physiology traits during exposure to an external stress

The electrochemical gradient of protons, or proton motive force (PMF), is at the heart of bacterial energetics. It consists of two components: the pH difference between a cell cytoplasm and the environment, and the membrane potential. The PMF powers such vital cellular processes as ATP production, motility and active membrane transport. The aim of this doctoral project was to relate the changes in the physiological state of the cell to the PMF in a variety of stressful environments and, using this, uncover the mechanisms through which these stresses induce cellular damage. In this thesis I have shown that by modelling an Escherichia coli cell as an electric circuit, the relationship between bacterial PMF, the electric properties of the cell membrane and the catabolism can be described mathematically. Subsequently, using the bacterial flagellar motor (BFM) as a single-cell "voltmeter" I have quantitatively described the effects of different stresses on the maintenance of cellular free energy. To achieve my goal I developed an assay for simultaneous monitoring of the PMF and the intracellular pH by using a combination of fluorescence and back-focal-plane (BFP) interferometry techniques. I confirmed the accuracy of the proposed approach by applying it to a known stress — indole treatment — and recovering the previously shown functional dependency between indole concentration and the membrane conductance. I then tested a variety of different stresses and found that butanol acts as an ionophore changing membrane conductance linearly with concentration and functionally characterised membrane damage caused by light of shorter wavelengths. I further proved that this light damage was mediated by reactive oxygen species by repeating light damage experiments in anaerobic conditions. Anaerobic conditions were also used for studying an acid challenge response where I demonstrated that the presence of oxygen is required for the maintenance of the cytoplasmic pH. Additionally, in the course of my project I tested and characterised several pH indicators. I demonstrated that the cpYFP sensor, previously used in eukaryotic cells, could be successfully used in E. coli to allow the internal pH measurements in the higher pH range, while the pHRed sensor was shown to form the aggregates in the cell cytoplasm and, consequently, to slow down the growth. The optimal protocol of the pH sensors calibration was established
The Effects of a Linguistic Tsunami on the Languages of Aceh

The languages throughout the world are in crisis and it is estimated that 50% to 90% will have disappeared by the end of this century (Grenoble, 2012). Colonisation, nationalism, urbanisation and globalisation have resulted in a linguistic tsunami being unleashed, with a few major world languages swamping others. The rate of language loss today is unprecedented as this small number of dominant languages expands rapidly. Small minority languages are mainly in danger, but even large regional languages, such as Acehnese with millions of speakers, are unsafe. Similar to the case of a tsunami triggered by an earthquake, it is generally too late before speakers are aware of what is happening. In most cases language shift will have already progressed and irreversible before people realize it. This paper examines the early warning signs of impending language shift and what can be done for minority languages to have the best chance of survival. We draw on the local situation in Aceh, as well as other parts of the Austronesian speaking world and Australia, where the record of language loss is the worst in the world. Language shift in Australia is well-progressed; in Indonesia it is more recent. Lessons learned from places such as Australia and Taiwan have relevance for Indonesia today.