Chemical composition and sensory profiling of coffees treated with asparaginase to decrease acrylamide formation during roasting.

Acrylamide is an amide formed in the Maillard reaction, with asparagine as the primary amino acid precursor. The intake of large amounts of acrylamide has induced genotoxic and carcinogenic effects in hormone-sensitive tissues of animals. The enzime asparaginase is one of the most effective methods for lowering the formation of acrylamide in foods such as potatoes. However, the reported sensory outcomes for coffee have been unsatisfactory so far. This study aimed to produce coffees with reduced levels of acrylamide by treating them with asparaginase while retaining their original sensory and bioactive profiles. Three raw samples of Coffea arabica, including two specialty coffees, and one of Coffea canephora were treated with 1000, 2000, and 3000 ASNU of the enzyme. Asparagine and bioactive compounds (chlorogenic acids-CGA, caffeine, and trigonelline) were quantified in raw and roasted beans by HPLC and LC-MS, while the determination of acrylamide and volatile organic compounds was performed in roasted beans by CG-MS. Soluble solids, titratable acidity, and pH were also determined. Professional cupping by Q-graders and consumer sensory tests were also conducted. Results were analyzed by ANOVA-Fisher, MFA, PCA and Cluster analyses, with significance levels set at p ≤ 0.05. Steam treatment alone decreased acrylamide content by 18.4%, on average, and 6.1% in medium roasted arabica and canefora coffees. Average reductions of 32.5-56.0% in acrylamide formation were observed in medium roasted arabica beans when 1000-3000 ASNU were applied. In the canefora sample, 59.4-60.7% reductions were observed. However, steam treatment primarily caused 17.1-26.7% reduction of total CGA and lactones in medium roasted arabica samples and 13.9-22.0% in canefora sample, while changes in trigonelline, caffeine, and other evaluated chemical parameters, including the volatile profiles were minimal. Increasing enzyme loads slightly elevated acidity. The only sensory changes observed by Q-graders and or consumers in treated samples were a modest increase in acidity when 3000 ASNU was used in the sample with lower acidity, loss of mild off-notes in control samples, and increased perception of sensory descriptors. The former was selected given the similarity in chemical outcomes among beans treated with 2000 and 3000 ASNU loads.

Effects of geographical origin and post-harvesting processing on the bioactive compounds and sensory quality of Brazilian specialty coffee beans.

Specialty coffee beans are those produced, processed, and characterized following the highest quality standards, toward delivering a superior final product. Environmental, climatic, genetic, and processing factors greatly influence the green beans' chemical profile, which reflects on the quality and pricing. The present study focuses on the assessment of eight major health-beneficial bioactive compounds in green coffee beans aiming to underscore the influence of the geographical origin and post-harvesting processing on the quality of the final beverage. For that, we examined the non-volatile chemical profile of specialty Coffea arabica beans from Minas Gerais state, Brazil. It included samples from Cerrado (Savannah), and Matas de Minas and Sul de Minas (Atlantic Forest) regions, produced by two post-harvesting processing practices. Trigonelline, theobromine, theophylline, chlorogenic acid derivatives, caffeine, caffeic acid, ferulic acid, and p-coumaric acid were quantified in the green beans by high-performance liquid chromatography with diode array detection. Additionally, all samples were roasted and subjected to sensory analysis for coffee grading. Principal component analysis suggested that Cerrado samples tended to set apart from the other geographical locations. Those samples also exhibited higher levels of trigonelline as confirmed by two-way ANOVA analysis. Samples subjected to de-pulping processing showed improved chemical composition and sensory score. Those pulped coffees displayed 5.8% more chlorogenic acid derivatives, with an enhancement of 1.5% in the sensory score compared to unprocessed counterparts. Multivariate logistic regression analysis pointed out altitude, ferulic acid, p-coumaric acid, sweetness, and acidity as predictors distinguishing specialty coffee beans obtained by the two post-harvest processing. These findings demonstrate the influence of regional growth conditions and post-harvest treatments on the chemical and sensory quality of coffee. In summary, the present study underscores the value of integrating target metabolite analysis with statistical tools to augment the characterization of specialty coffee beans, offering novel insights for quality assessment with a focus on their bioactive compounds.

Online consumer testing beyond central location tests: A case study for brewed coffee.

Due to the constraints of the COVID-19 pandemic, conducting sensory evaluations requiring direct interactions became challenging. In response, researchers have been motivated to devise non-face-to-face testing methods as alternatives. This study aimed to compare two non-face-to-face home-use tests (HUT) with the traditional face-to-face central location test (CLT). Both HUTs involved online recruitment and sample delivery to participants' homes. One HUT provided a written protocol with no direct interaction (contactless HUT; C-HUT), whereas the other included an online meeting with a researcher for live guidance (online HUT; O-HUT). Four coffee samples were evaluated on the basis of liking and sensory and emotional attributes. The comparison between CLT and O-HUT showed RV coefficients of 0.92, 0.93, and 0.98 (P < 0.05) for liking and sensory and emotional attributes, respectively. In addition, based on the RV coefficient, the CLT results showed a significantly greater similarity to those of O-HUT compared to those of C-HUT. The O-HUT also outperformed the C-HUT in its ability to significantly discriminate between samples. Hence, real-time interactions between researchers and participants, as facilitated by O-HUT, may be more suitable in certain scenarios compared to C-HUT, which relies solely on a written protocol. Overall, these findings suggest that C-HUT and O-HUT are suitable methods for collecting sensory data and overcoming geographic and face-to-face contact limitations, providing greater flexibility, and reducing the time and cost associated with traditional sensory evaluations.

From cup to clock: exploring coffee's role in slowing down biological aging.

Background: Previous research has proposed that coffee consumption may have potential health benefits, yet the effect of coffee on one's biological age has not been determined to date. The purpose of this study is to investigate the influence of coffee drinking on biological aging. Methods: Participants were chosen from the National Health and Nutrition Examination Survey (NHANES) and had to meet the selection criteria. Coffee consumption was evaluated through two 24-hour dietary questionnaires. Biological age was measured using both the PhenoAge and KDM-BA algorithms. Multiple linear and logistic regression models were adopted to analyze the association of coffee consumption with biological aging. Results: A total of 13 384 participants with an average daily coffee consumption of 1.73 cups were included. Participants with higher coffee consumption tended to be older, male, non-Hispanic white; had a higher educational level beyond high school; were more likely to be married; had better financial status; and were less likely to smoke or engage in excessive drinking. These individuals with higher coffee consumption exhibited a younger biological age in relation to their chronological age, as indicated by lower mean advancements in PhenoAge and KDM-BA scores. Furthermore, coffee intake was found to be inversely related to PhenoAge and KDM-BA progressions, as well as to the chances of accelerated biological aging, both in unadjusted and adjusted models. These associations remained consistent across all age and gender groups. Additionally, some heterogeneity was also observed among body mass index and physical activity categories. Conclusions: Coffee drinking was inversely related to biological age advancements and the likelihood of accelerated biological aging. Moderate coffee consumption may offer substantial benefits in reducing biological aging.

Association of tea and coffee consumption and biliary tract cancer risk: The Biliary Tract Cancers Pooling Project.

BACKGROUND AND AIMS: Tea and coffee are widely consumed beverages worldwide. We evaluated their association with biliary tract cancer (BTC) incidence. APPROACH AND RESULTS: We pooled data from 15 studies in the Biliary Tract Cancers Pooling Project to evaluate associations between tea and coffee consumption and biliary tract cancer development. We categorized participants as nondrinkers (0 cup/day), moderate drinkers (>0 and <3 cups/day), and heavy drinkers (≥3 cups/day). We estimated multivariable HRs and 95% CIs using Cox models. During 29,911,744 person-years of follow-up, 851 gallbladder, 588 intrahepatic bile duct, 753 extrahepatic bile duct, and 458 ampulla of Vater cancer cases were diagnosed. Individuals who drank tea showed a statistically significantly lower incidence rate of gallbladder cancer (GBC) relative to tea nondrinkers (HR=0.77; 95% CI, 0.64-0.91), and intrahepatic bile duct cancer (IHBDC) had an inverse association (HR=0.81; 95% CI, 0.66-1.00). However, no associations were observed for extrahepatic bile duct cancer (EHBDC) or ampulla of Vater cancer (AVC). In contrast, coffee consumption was positively associated with GBC, with a higher incidence rate for individuals consuming more coffee (HR<3 cups/day =1.29; 95% CI, 1.01-1.66; HR≥3 cups/day =1.49; 95% CI, 1.11-1.99, Ptrend=0.01) relative to coffee nondrinkers. However, there was no association between coffee consumption and GBC when restricted to coffee drinkers. There was little evidence of associations between coffee consumption and other biliary tract cancers. CONCLUSIONS: Tea consumption was associated with a lower incidence of GBC and possibly IHBDC. Further research is warranted to replicate the observed positive association between coffee and GBC.

Effect of fluoride or chitosan toothpaste and at-home bleaching in enamel roughness, tooth color, and staining susceptibility.

PURPOSE: To evaluate how fluoride- or chitosan-based toothpaste used during at-home bleaching affects enamel roughness, tooth color, and staining susceptibility. METHODS: Bovine enamel blocks were submitted to a 14-day cycling regime considering a factorial design (bleaching agent x toothpaste, 2 x 3), with n=10: (1) bleaching with 16% carbamide peroxide (CP) or 6% hydrogen peroxide (HP), and (2) daily exposure of a fluoride (1,450 ppm F-NaF) toothpaste (FT), chitosan-based toothpaste (CBT), or distilled water (control). Then, 24 hours after the last day of bleaching procedure the samples were exposed to a coffee solution. Color (ΔEab, ΔE00, L*, a*, b*) and roughness (Ra, µm) analyses were performed to compare the samples initially (baseline), after bleaching, and after coffee staining. The results were evaluated by linear models for repeated measures (L*, a*, b*, and Ra), 2-way ANOVA (ΔEab, ΔE00) and Tukey's test (α= 0.05). RESULTS: After the at-home bleaching procedure (toothpaste vs. time, P< 0.0001), the toothpaste groups presented a statistically lower Ra than the control (CBT 0.05). After coffee exposure, CBT presented lower ΔEab and ΔE00 values in the HP groups (toothpaste, P< 0.0001), and lower b* and a* values in the CP groups (toothpaste vs. time, P= 0.004). CLINICAL SIGNIFICANCE: Fluoride or chitosan delivered by toothpaste can reduce surface alterations of the enamel during at-home bleaching, without affecting bleaching efficacy.

Mendelian randomization reveals the impact of diet on infertility in men and women.

Background: Although studies on the effects of diet on fertility has progressed, some cumulative evidence has piled against popular hypotheses. The aim of our study was to investigate the effects of 31 diets including 23 individual dietary intakes and 8 dietary habits on infertility in men and women. Methods: The datas of diets and infertility were collected from genome-wide association studies (GWAS). Mendelian randomization (MR) methods were used to analyze causal relationships. Multivariate MR (MVMR) adjusted for the effects of other exposures on causality. And MR-Egger, Cochran's Q, radial MR, and MR-PRESSO tests were employed to assess heterogeneity and horizontal pleiotropy. Results: Our study found that coffee intake (OR, 3.6967; 95% CI, 1.0348 - 13.2065; P = 0.0442) and cooked vegetable intakes (OR, 54.7865; 95% CI, 2.9011 - 1030.5500; P = 0.0076) increased the risk of male infertility. For women, beer was a risk factor for infertility (OR, 4.0932; 95% CI, 1.8728 - 8.9461; P = 0.0004); but processed meat was negatively associated with infertility (OR, 0.5148; 95% CI, 0.2730 - 0.9705; P = 0.0401). MVMR demonstrated selenium as a protective factor against female infertility (OR, 7.4474e-12; 95% CI, 5.4780e-22 - 1.0125e-01; P = 0.0314). Conclusion: We found the causal relationships between four diets and infertility. We look forward to more high-quality epidemiologic studies to prove our conclusions.

Color Stability of Bioactive Restorative Material vs Nanohybrid Resin Composite: An In Vitro Study.

AIM: This study aimed to assess the color stability of bioactive restorative materials vs nanohybrid resin composites after 3 months of immersion in three frequently consumed beverages. MATERIALS AND METHODS: Thirty disk-shaped specimens of Giomer dental restorative material (Shofu, Japan) and nanohybrid resin composite (Tokuyama, Japan) were performed using a Teflon mold. Super-Snap system (Shofu, Japan) was utilized to finish and polish the specimens to be preserved for 24 hours in distilled water at 37°C. The samples had been divided into three subgroups (Coffee, tea, Pepsi) (n = 5). The initially displayed color measurements of the samples were performed using a spectrophotometer (VITA Easyshade® V). After 7 days, 30 days, and 90 days, color measurements were repeated, and the E of each sample was estimated. E of each sample was calculated. RESULTS: The Giomer group showed statistically significant higher E values than the nanohybrid resin composite where the p-value was ≤0.0001. Tea subgroup showed the highest statistically significant E values in both groups where the p-value was ≤ 0.0001. The highest statistically significant color change was recorded at 3 months. CONCLUSION: The color of bioactive restorative material is less stable if compared with nanohybrid resin composite. CLINICAL SIGNIFICANCE: As tea and coffee are popular beverages, particularly in Middle Eastern nations, dentists must advise patients about the color change of resin restorations. Patients are advised to brush their teeth immediately after consuming these beverages. How to cite this article: Saber EH, Abielhassan MH, Abed YA, et al. Color Stability of Bioactive Restorative Material vs Nanohybrid Resin Composite: An In Vitro Study. J Contemp Dent Pract 2024;25(3):221-225.

Use of different dry materials to control the moisture in a black soldier fly (Hermetia illucens) rearing substrate.

Background: Controlling the substrate moisture is a significant challenge in black soldier fly (BSF) farming. Many substrates have a high moisture content, which results in a low BSF biomass and a high mortality. One potential solution involves incorporating dry substrates into the food mix to mitigate the excessive moisture. However, little information about the types and quantities of dry substrates is available. Methods: Six different dry materials-rice husk (RH), rice bran (RB), rice husk ash (RHA), coconut coir dust (CC), rubberwood sawdust (RSD), and spent coffee grounds (SCGs)-were evaluated by combining with pure minced mixed vegetables in varying proportions (0%, 5%, 10%, 15%, 25%, and 50% by weight). This study encompassed both small-scale and medium-scale experiments to comprehensively assess the effects of the addition of each of these different dry substrates and their quantities on aspects of the development of BSF, such as BSF biomass, larval duration, mortality rates, adult sex ratio, and the moisture removal efficiency of each substrate mixture. Results: Each dry substrate had specific properties. Although RB emerged as a favorable dry substrate owing to its nutritional content and substantial water-holding capacity, excessive use of RB (>15% by weight) resulted in elevated temperatures and subsequent desiccation of the substrate, potentially leading to larval mortality. In contrast, RH demonstrated the ability to support improved larval duration and growth, permitting its utilization in higher proportions (up to 50%). On the other hand, CC, RHA, and SCG are better suited for inclusion in BSF larval substrates in smaller quantities. Discussion: Some dry substrates require a pretreatment process to eliminate toxic substances prior to their incorporation into substrate mixtures, such as CC and SCG. A potential alternative solution involves employing a combination of various dry substrates. This approach aims to enhance the substrate moisture control and subsequently improve the BSF rearing performance.

Association of coffee intake with bone mineral density: a Mendelian randomization study.

Background: In observational studies, the relationship between coffee intake and bone mineral density (BMD) is contradictory. However, residual confounding tends to bias the results of these studies. Therefore, we used a two-sample Mendelian randomization (MR) approach to further investigate the potential causal relationship between the two. Methods: Genetic instrumental variables (IVs) associated with coffee intake were derived from genome-wide association studies (GWAS) of the Food Frequency Questionnaire (FFQ) in 428,860 British individuals and matched using phenotypes in PhenoScanner. Summarized data on BMD were obtained from 537,750 participants, including total body BMD (TB-BMD), TB-BMD in five age brackets ≥60, 45-60, 30-45, 15-30, and 0-15 years, and BMD in four body sites: the lumbar spine, the femoral neck, the heel, and the ultradistal forearm. We used inverse variance weighting (IVW) methods as the primary analytical method for causal inference. In addition, several sensitivity analyses (MR-Egger, Weighted median, MR-PRESSO, Cochran's Q test, and Leave-one-out test) were used to test the robustness of the results. Results: After Bonferroni correction, Coffee intake has a potential positive correlation with total body BMD (effect estimate [Beta]: 0.198, 95% confidence interval [Cl]: 0.05-0.35, P=0.008). In subgroup analyses, coffee intake was potentially positively associated with TB-BMD (45-60, 30-45 years) (Beta: 0.408, 95% Cl: 0.12-0.69, P=0.005; Beta: 0.486, 95% Cl: 0.12-0.85, P=0.010). In addition, a significant positive correlation with heel BMD was also observed (Beta: 0.173, 95% Cl: 0.08-0.27, P=0.002). The results of the sensitivity analysis were generally consistent. Conclusion: The results of the present study provide genetic evidence for the idea that coffee intake is beneficial for bone density. Further studies are needed to reveal the biological mechanisms and offer solid support for clinical guidelines on osteoporosis prevention.

Assessing scale-dependency of climate risks in coffee-based agroforestry systems.

Agroforestry is a management strategy for mitigating the negative impacts of climate and adapting to sustainable farming systems. The successful implementation of agroforestry strategies requires that climate risks are appropriately assessed. The spatial scale, a critical determinant influencing climate impact assessments and, subsequently, agroforestry strategies, has been an overlooked dimension in the literature. In this study, climate risk impacts on robusta coffee production were investigated at different spatial scales in coffee-based agroforestry systems across India. Data from 314 coffee farms distributed across the districts of Chikmagalur and Coorg (Karnataka state) and Wayanad (Kerala state) were collected during the 2015/2016 to 2017/2018 coffee seasons and were used to quantify the key climate drivers of coffee yield. Projected climate data for two scenarios of change in global climate corresponding to (1) current baseline conditions (1985-2015) and (2) global mean temperatures 2 °C above preindustrial levels were then used to assess impacts on robusta coffee yield. Results indicated that at the district scale rainfall variability predominantly constrained coffee productivity, while at a broader regional scale, maximum temperature was the most important factor. Under a 2 °C global warming scenario relative to the baseline (1985-2015) climatic conditions, the changes in coffee yield exhibited spatial-scale dependent disparities. Whilst modest increases in yield (up to 5%) were projected from district-scale models, at the regional scale, reductions in coffee yield by 10-20% on average were found. These divergent impacts of climate risks underscore the imperative for coffee-based agroforestry systems to develop strategies that operate effectively at various scales to ensure better resilience to the changing climate.

An exploratory study to assess the knowledge, attitudes and practices of Lebanese residents towards acrylamide.

INTRODUCTION: For years, heat treatment has been an essential method for ensuring mature food that meet the desired quality and safety characteristics. However, this process could lead to the formation of harmful compounds such as acrylamide. In this study we aimed to investigate the knowledge, attitudes and practices (KAPs) of the Lebanese population toward the potential risk associated with acrylamide. MATERIALS & METHODS: An online survey (n = 598) was conducted among residents in Lebanon aged 18 years and above. The survey was divided into five sections including participants' sociodemographic characteristics, knowledge, attitude and practice sections, and some questions related to consumer's preferences. RESULTS & DISCUSSION: The results showed that the majority of the participants had low food safety knowledge regarding acrylamide. Specifically, 82.9% of the consumers had no idea about the chemical, its formation, the foods with a high risk of acrylamide formation and the health risks associated with its exposure. Despite lack of knowledge, good domestic food practices (storage, pre-treatment) were noticed among participants. Moreover, the majority of consumers (> 80%) showed positive attitude towards proper acrylamide labeling. Participants with a bachelor's degree appeared to have a more positive attitude toward food safety compared to those with no qualifications (p<0.001). CONCLUSION: Despite the high consumption of acrylamide by the consumers in Lebanon through fried potatoes, bread, and coffee, the majority have no idea about acrylamide's presence in food, its sources and its adverse health effects. Raising awareness among the public, involving policy makers in addressing the issue of clear labeling and encouraging the adoption of alternative practices to reduce acrylamide are all crucial to protect consumers' health in Lebanon and promote healthier food consumption habits.

Edge based metric dimension of various coffee compounds.

An important dietary source of physiologically active compounds, coffee also contains phenolic acids, diterpenes, and caffeine. According to a certain study, some coffee secondary metabolites may advantageously modify a number of anti-cancer defense systems. This research looked at a few coffee chemical structures in terms of edge locating numbers or edge metric size to better understand the mechanics of coffee molecules. Additionally, this research includes graph theoretical properties of coffee chemical structures. The chemicals found in coffee, such as caffeine, diterpene or cafestol, kahweol, chlorogenic, caffeic, gallotannins, and ellagitannins, are especially examined in these publications.

Oral Antiviral Defense: Saliva- and Beverage-like Hypotonicity Dynamically Regulate Formation of Membraneless Biomolecular Condensates of Antiviral Human MxA in Oral Epithelial Cells.

The oral mucosa represents a defensive barrier between the external environment and the rest of the body. Oral mucosal cells are constantly bathed in hypotonic saliva (normally one-third tonicity compared to plasma) and are repeatedly exposed to environmental stresses of tonicity, temperature, and pH by the drinks we imbibe (e.g., hypotonic: water, tea, and coffee; hypertonic: assorted fruit juices, and red wines). In the mouth, the broad-spectrum antiviral mediator MxA (a dynamin-family large GTPase) is constitutively expressed in healthy periodontal tissues and induced by Type III interferons (e.g., IFN-λ1/IL-29). Endogenously induced human MxA and exogenously expressed human GFP-MxA formed membraneless biomolecular condensates in the cytoplasm of oral carcinoma cells (OECM1 cell line). These condensates likely represent storage granules in equilibrium with antivirally active dispersed MxA. Remarkably, cytoplasmic MxA condensates were exquisitely sensitive sensors of hypotonicity-the condensates in oral epithelium disassembled within 1-2 min of exposure of cells to saliva-like one-third hypotonicity, and spontaneously reassembled in the next 4-7 min. Water, tea, and coffee enhanced this disassembly. Fluorescence changes in OECM1 cells preloaded with calcein-AM (a reporter of cytosolic "macromolecular crowding") confirmed that this process involved macromolecular uncrowding and subsequent recrowding secondary to changes in cell volume. However, hypertonicity had little effect on MxA condensates. The spontaneous reassembly of GFP-MxA condensates in oral epithelial cells, even under continuous saliva-like hypotonicity, was slowed by the protein-phosphatase-inhibitor cyclosporin A (CsA) and by the K-channel-blocker tetraethylammonium chloride (TEA); this is suggestive of the involvement of the volume-sensitive WNK kinase-protein phosphatase (PTP)-K-Cl cotransporter (KCC) pathway in the regulated volume decrease (RVD) during condensate reassembly in oral cells. The present study identifies a novel subcellular consequence of hypotonic stress in oral epithelial cells, in terms of the rapid and dynamic changes in the structure of one class of phase-separated biomolecular condensates in the cytoplasm-the antiviral MxA condensates. More generally, the data raise the possibility that hypotonicity-driven stresses likely affect other intracellular functions involving liquid-liquid phase separation (LLPS) in cells of the oral mucosa.

Dietary total antioxidant capacity of Moroccan Type 2 Diabetes Mellitus patients.

AIMS: A new approach to a healthy diet is the assessment of dietary Total Antioxidant Capacity (TAC). The aim of this study was to assess the dietary TAC among Moroccan Type 2 Diabetes Mellitus (T2DM) patients and identify the main food sources contributing to the total antioxidant capacity intake. METHODS: A total of 254 patients with T2DM was included in the study. The usual dietary intakes were assessed by means of a validated food frequency questionnaire. The dietary TAC was estimated using published databases of the antioxidant content of foods measured by the FRAP (ferric ion reducing antioxidant potential) method. RESULTS: The mean (SD) dietary TAC of the studied type 2 diabetes patients was 10.86 (3.42) mmol/day. Correlation analyses showed a positive association between dietary TAC and the consumption of healthy food groups, such as fruits and vegetables. Tea and coffee beverages (38.6%), vegetables (21.9%), cereals and pulses (18.8%), fruits and fruit juices (12.4%) were major food sources of dietary antioxidant intake. The relatively short list of twenty food items that contributed most to dietary TAC presented an important explanation of roughly 94%. These included tea, coffee, broad beans, artichoke, pepper, beetroot, sweet potatoes, pomegranate, mandarin, figs, strawberry, orange juice, olives, cashew nuts, almonds, sunflower seeds, dchicha and white beans. CONCLUSIONS: This study supplies baseline dietary TAC data for Moroccan T2DM patients that may help to elucidate which aspects of the eating habits and behaviours require improvement and provide the opportunity to develop dietary guidelines as part of the nutritional diabetes management.

Haitian coffee agroforestry systems harbor complex arabica variety mixtures and under-recognized genetic diversity.

Though facing significant challenges, coffee (Coffea arabica) grown in Haitian agroforestry systems are important contributors to rural livelihoods and provide several ecosystem services. However, little is known about their genetic diversity and the variety mixtures used. In light of this, there is a need to characterize Haitian coffee diversity to help inform revitalization of this sector. We sampled 28 diverse farms in historically important coffee growing regions of northern and southern Haiti. We performed KASP-genotyping of SNP markers and HiPlex multiplex amplicon sequencing for haplotype calling on our samples, as well as several Ethiopian and commercial accessions from international collections. This allowed us to assign Haitian samples to varietal groups. Our analyses revealed considerable genetic diversity in Haitian farms, higher in fact than many farmers realized. Notably, genetic structure analyses revealed the presence of clusters related to Typica, Bourbon, and Catimor groups, another group that was not represented in our reference accession panel, and several admixed individuals. Across the study areas, we found both mixed-variety farms and monovarietal farms with the historical and traditional Typica variety. This study is, to our knowledge, the first to genetically characterize Haitian C. arabica variety mixtures, and report the limited cultivation of C. canephora (Robusta coffee) in the study area. Our results show that some coffee farms are repositories of historical, widely-abandoned varieties while others are generators of new diversity through genetic mixing.

Effects of various beverages on characteristics of provisional restoration materials.

OBJECTIVE: To investigate the effect of common beverages on four currently used provisional restoration materials: Protemp®4, Integrity®, polymethyl methacrylate (PMMA) block, and acrylic resin. Flowable resin composite is included as a control group. MATERIALS AND METHODS: Each material was formed into disks of 10-mm diameter and 4-mm thickness (N = 40) by loading the material into acrylic molds. The exposed surface in the mold was covered using a glass slide to prevent an oxygen inhibition layer, and polymerization then proceeded. The solidified disks were placed in distilled water for 24 h. These samples (n = 8) were then immersed for 14 days in one of four different beverages: water, orange juice, cola, and coffee. Changes in color dimension, hardness, and roughness were observed and then analyzed using two-way repeated analysis of variance. RESULTS: The provisional materials had more obvious changes in all three color dimensions than the flowable resin composite. Integrity showed the biggest changes, followed by acrylic resin and PMMA block, whereas Protemp had the smallest changes. The hardness of all the materials significantly decreased after immersion in any of the beverages for 14 days. There were no changes in surface roughness when the materials were immersed in distilled water. The surface roughness of the PMMA block significantly decreased in orange juice whereas that of Integrity and acrylic resin significantly increased in cola. CONCLUSION: Different kinds of provisional materials had different degrees of staining due to their composition. Moisture had a significant influence on the hardness of materials, and the acidity of cola significantly roughened the surface of the provisional materials.

The causal association between artificial sweeteners and the risk of cancer: a Mendelian randomization study.

Artificial sweeteners (ASs) have been widely added to food and beverages because of their properties of low calories and sweet taste. However, whether the consumption of ASs is causally associated with cancer risk is not clear. Here, we utilized the two-sample Mendelian randomization (MR) method to study the potential causal association. Genetic variants like single-nucleotide polymorphisms (SNPs) associated with exposure (AS consumption) were extracted from a genome-wide association study (GWAS) database including 64 949 Europeans and the influence of confounding was removed. The outcome was from 98 GWAS data and included several types of cancers like lung cancer, colorectal cancer, stomach cancer, breast cancer, and so on. The exposure-outcome SNPs were harmonized and then MR analysis was performed. The inverse-variance weighted (IVW) with random effects was used as the main analytical method accompanied by four complementary methods: MR Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses consisted of heterogeneity, pleiotropy, and leave-one-out analysis. Our results demonstrated that ASs added to coffee had a positive association with high-grade and low-grade serous ovarian cancer; ASs added to tea had a positive association with oral cavity and pharyngeal cancers, but a negative association with malignant neoplasm of the bronchus and lungs. No other cancers had a genetic causal association with AS consumption. Our MR study revealed that AS consumption had no genetic causal association with major cancers. Larger MR studies or RCTs are needed to investigate small effects and support this conclusion.

TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments.

Accurate multiple sequence alignment (MSA) is imperative for the comprehensive analysis of biological sequences. However, a notable challenge arises as no single MSA tool consistently outperforms its counterparts across diverse datasets. Users often have to try multiple MSA tools to achieve optimal alignment results, which can be time-consuming and memory-intensive. While the overall accuracy of certain MSA results may be lower, there could be local regions with the highest alignment scores, prompting researchers to seek a tool capable of merging these locally optimal results from multiple initial alignments into a globally optimal alignment. In this study, we introduce Two Pointers Meta-Alignment (TPMA), a novel tool designed for the integration of nucleic acid sequence alignments. TPMA employs two pointers to partition the initial alignments into blocks containing identical sequence fragments. It selects blocks with the high sum of pairs (SP) scores to concatenate them into an alignment with an overall SP score superior to that of the initial alignments. Through tests on simulated and real datasets, the experimental results consistently demonstrate that TPMA outperforms M-Coffee in terms of aSP, Q, and total column (TC) scores across most datasets. Even in cases where TPMA's scores are comparable to M-Coffee, TPMA exhibits significantly lower running time and memory consumption. Furthermore, we comprehensively assessed all the MSA tools used in the experiments, considering accuracy, time, and memory consumption. We propose accurate and fast combination strategies for small and large datasets, which streamline the user tool selection process and facilitate large-scale dataset integration. The dataset and source code of TPMA are available on GitHub (https://github.com/malabz/TPMA).