Miracle-dz/UniFAR-FTUs huggingface dataset:
Is the Straight Leg Raise Suitable for the Diagnosis of Radiculopathy? Analysis of Diagnostic Accuracy in a Phase III Study

The straight leg raise test (SLR) has been proposed to detect increased nerve mechanosensitivity of the lower limbs in individuals with low back pain. However, its validity in the diagnosis of lumbosacral radiculopathy shows very variable results. The aim of this study was to analyse the diagnostic validity of the SLR including well-defined diagnostic criteria (a change in symptoms with the structural differentiation manoeuvre and the reproduction of the patient’s symptoms during the test or the asymmetries in the range of motion or symptoms location between limbs) in a sample of participants in phase III with suspicion of lumbar radiculopathy using the electrodiagnostic studies (EDX) as the reference standard. A phase III diagnostic accuracy study was designed. In total, 142 individuals with suspected lumbosacral radiculopathy referred for EDX participated in the study. Each participant was tested with EDX and SLR. SLR was considered positive using three diagnostic criteria. The sensitivity of the SLR for Criterion 3 was 89.02% (CI 81.65–96.40), the specificity was 25.00% (CI 13.21–36.79), and the positive and negative likelihood ratios were 1.19 (CI 1.01–1.40) and 0.44 (0.21–0.94), respectively. SLR showed limited validity in the diagnosis of lumbosacral radiculopathy. The incorporation of more objective diagnostic criteria (asymmetry in range of motion or localisation of symptoms) improved the diagnostic validity but the imprecision of the confidence intervals limited the interpretation of the results.
Constitutive Behavior of Olivine Gouge Across the Brittle‐Ductile Transition

The bottom of the lithosphere is characterized by a thermally controlled transition from brittle to ductile deformation. While the mechanical behavior of rocks firmly within the brittle and ductile regimes is relatively well understood, how the transition operates remains elusive. Here, we study the mechanical properties of pure olivine gouge from 100 to 500°C under 100 MPa pore‐fluid pressure in a triaxial deformation apparatus as a proxy for the mechanical properties of the upper mantle across the brittle‐ductile transition. We describe the mechanical data with a rate‐, state‐, and temperature‐dependent constitutive law with multiple thermally activated deformation mechanisms. The stress power exponents decrease from 70 ± 10 in the brittle regime to 17 ± 3 and 4 ± 2 in the semi‐brittle and ductile regimes, respectively. The mechanical model consistently explains the mechanical behavior of olivine gouge across the brittle‐ductile transition, capturing the gradual evolution from cataclasis to crystal plasticity.
Creating high-resolution 3D cranial implant geometry using deep learning techniques

Creating a personalized implant for cranioplasty can be costly and aesthetically challenging, particularly for comminuted fractures that affect a wide area. Despite significant advances in deep learning techniques for 2D image completion, generating a 3D shape inpainting remains challenging due to the higher dimensionality and computational demands for 3D skull models. Here, we present a practical deep-learning approach to generate implant geometry from defective 3D skull models created from CT scans. Our proposed 3D reconstruction system comprises two neural networks that produce high-quality implant models suitable for clinical use while reducing training time. The first network repairs low-resolution defective models, while the second network enhances the volumetric resolution of the repaired model. We have tested our method in simulations and real-life surgical practices, producing implants that fit naturally and precisely match defect boundaries, particularly for skull defects above the Frankfort horizontal plane.
First-Generation Cephalosporins for Treatment of Acute Hematogenous Osteomyelitis in Children: A Study of Efficacy and Adverse Effects

Abstract Background Acute hematogenous osteomyelitis (AHO) is a relatively infrequent but significant infection in pediatric patients. As Staphylococcus aureus is the most common cause of AHO, intravenous and oral first-generation cephalosporins are common therapies. Cephalexin is a commonly prescribed oral therapy for pediatric AHO, although it requires frequent dosing that may affect adherence. Cefadroxil is a comparable oral first-generation cephalosporin with a more desirable dosing schedule. Methods We reviewed pediatric patients admitted to Mayo Clinic between March 2002 and September 2020 for management of AHO who received treatment with a first-generation cephalosporin. We reviewed timing of oral therapy transition, therapy-associated adverse effects, and recurrence of disease after completion of therapy. Results There were 59 patients included in the study. There was similar occurrence of adverse effects in patients receiving cefadroxil and cephalexin, although use of cefadroxil coincided with more gastrointestinal adverse effects and leukopenia and use of cephalexin with more rash and neutropenia. One secondary treatment failure occurred in our study, in a patient receiving cephalexin for treatment of septic arthritis. Conclusions Cefadroxil may be a reasonable alternative oral therapy for methicillin-susceptible S aureus or culture-negative AHO in pediatric patients, particularly when a less frequent dosing schedule is desired. Future study with a larger sample size is warranted.
COMPARISON OF KELAKAI AND KATUK EXTRACT COMBINATION TO 0.2% CHLORHEXIDINE GLUCONATE AGAINST Porphyromonas gingivalis

Background: Periodontal disease is the second most frequent oral disease in Indonesia, which includes periodontitis. Porphyromonas gingivalis is the predominant bacteria in chronic periodontitis. This disease is usually treated with 0.2% chlorhexidine gluconate mouthwash. However, 0.2% chlorhexidine gluconate has several adverse effects, such as tooth discoloration, irritation of the oral mucosa, and changes in taste sensation. Therefore, an herbal-based mouthwash is needed. A combination of kelakai leaf and katuk leaf extract contains antibacterial substances such as flavonoid, tannin, steroid, alkaloid, and saponin, which can be used as an alternative therapy for chronic periodontitis. Purpose: To compare the inhibitory zone of kelakai and katuk extract combination with 0.2 Chlorhexidine gluconate against Porphyromonas gingivalis. Method: True experimental design with 13 treatment groups and 3 repetitions for each group. The treatment groups include combinations of kelakai leaf extract with 25%, 50%, 75%, 100% concentrations and katuk leaf extract with 20%, 40%, 80% concentrations and 0.2% chlorhexidine gluconate, which were tested on Porphyromonas gingivalis with a total of 39 samples. The inhibitory zone is measured with caliper after incubated for 48 hours. Results: One-Way ANOVA revealed significant differences between all treatment groups and 0.2% chlorhexidine gluconate. Consequently, the Bonferroni post-hoc test was performed, which showed that the antibacterial activity of 75% kelakai leaf and 80% katuk leaf extract did not differ significantly from the activity of 0.2% chlorhexidine gluconate. Conclusion: The combination of 75% kelakai leaf and 80% katuk leaf extract has an equal antibacterial activity to 0.2% chlorhexidine gluconate against Porphyromonas gingivalis statistically. Keywords : 0.2 % Chlorhexidine gluconate, chronic periodontitis, combination of kelakai and katuk leaf extract, inhibitory activity, Porphyromonas gingivalis
Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data

Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.
Inflammatory indices as prognostic markers in metastatic colorectal cancer patients treated with chemotherapy plus Bevacizumab

Background: Validated predictors of sensitivity or resistance to Bevacizumab (Bev) are not available, and Inflammatory Indexes (IIs) has been reported to be useful prognostic factors in various malignant solid tumours, including metastatic colorectal cancer (mCRC). Objectives: To explore the prognostic value of IIs in mCRC patients treated with first-line chemotherapy plus Bev. Design: One hundred and eighty-two patients diagnosed with mCRC and treated with first line chemotherapy plus Bev were considered for this prospective non-pharmacological study. Neutrophil, lymphocyte, platelet, aspartate transaminase (AST) and lactate dehydrogenase (LDH) tests were carried out at baseline and before each treatment cycle, according to clinical practice. Methods: Pre-treatment Systemic Immune-inflammation Index (SII), Colon Inflammatory Index (CII) and Aspartate aminotransferase-Lymphocyte Ratio Index (ALRI) were evaluated to assess a correlation with progression-free survival (PFS) and overall survival (OS). Results: In the overall population, PFS and OS were lower in patients with high SII (HR 1.64, p = 0.006 and HR 1.75, p = 0.004, respectively) and high ALRI (HR 2.13, p = 0.001 and HR 1.76, p = 0.02, respectively), but no difference was detected according to CII value. The multivariate analysis confirmed both SII and ALRI as independent prognostic factors for PFS (HR 1.64 and 2.82, respectively) and OS (HR 1.65 and 2.12, respectively). Conclusion: Our results demonstrate and confirm that IIs, and in particular SII and ALRI, are easy to measure prognostic markers for patient candidates to first line chemotherapy plus Bev for mCRC.
Biological, Nutritional, and Processing Factors Affecting Breast Meat Quality of Broilers

A study was conducted to investigate the effects of genetic strain, plane of nutrition, and age at slaughter on performance and meat quality traits of broiler chickens. A total of 2,160 broilers from two commercial lines selected either for rapid growth (BODY) or breast meat yield (BREAST) were fed two diets formulated to provide a low (LPN) and a high (HPN) plane of nutrition. The diets were isocaloric but differed in crude protein (CP) content, with the HPN diets providing higher protein levels at the starter, grower, and finisher stages of the growing phase than the LPN rations. Broilers were grown from hatch to 53 d and BW was measured at hatch, 19, 42, and 53 d of age. Broilers of the BODY line were significantly heavier at hatch, 19, and 42 d, but were not different from the BREAST line at 53 d. The HPN diets significantly increased BW in both lines at 19 and 42 d, but there were no diet effects at 53 d. There were no significant line by diet interactions for BW at any age. To evaluate carcass and meat quality traits, 108 birds were processed at 42 and 53 d. Carcasses were chilled in ice-water (0° C) overnight. Breast muscle samples were taken at . 25, 4, and 24 h postmortem (PM) for pH and R-value determination. At 24 h, breast fillets were harvested and evaluated for color (L*, a* and b* values), water holding capacity (WHC), and expressible moisture (EM). In addition, breast muscle temperature was monitored from . 25 to 10 h PM. There were no significant line or diet differences in live or carcass weights. However, breast muscle weight (BMW), breast meat yield (BMY) and carcass yields were significantly greater for the BREAST than BODY birds. The HPN significantly increased BMW and BMY in both lines, but no differences in carcass yields were observed. As age of the bird increased, live BW, carcass weight and yields, BMW, and BMW also increased. Breast muscle temperature declined from 40.3° C at . 25 h to 2.5° C at 3 h PM, after which temperatures remained below 2.5° C. Temperature decline was similar for all birds regardless of strain, diet, and age. Breast fillets of the BREAST line birds had lower pH (24 h), higher R-value (24 h), greater L*, a*, and b* values, lower WHC, and higher EM when compared with those of the BODY line fillets. Breast fillets from birds processed
2023 Korean Association of Urogenital Tract Infection and Inflammation guidelines for gonococcal infection

The incidence of gonorrhea has increased significantly in recent years in the United States, especially among sexually active twenty-year-olds. Although the incidence of gonorrhea has decreased in Korea since the early 2000s, it is still common among people in their twenties. Nucleic acid amplification test (NAAT) is the most sensitive diagnostic test for detecting gonococcal infection. Gram-staining is a simple and useful laboratory test for diagnosing symptomatic male gonococcal urethritis. Although bacterial culture can be used to detect antimicrobial susceptibility, its sensitivity is lower than that of NAAT. Treatment for uncomplicated gonorrhea infection is a single intramuscular injection of ceftriaxone 500 mg. Doxycycline (100 mg twice daily for 7 days) is added if there is a possibility of co-infection with chlamydia. If ceftriaxone is difficult to use, spectinomycin 2 g can be injected intramuscularly in Korea. Patients with gonorrhea should have repeated examinations within three months at the exposure site because of a high risk of re-infection. A person diagnosed with gonorrhea should discuss the nature of the infection, the importance of informing partners, when sexual activity can resume, and how to reduce the risk of sexually transmitted infections.
Culture media influences Candida parapsilosis growth, susceptibility, and virulence

Introduction Candida parapsilosis, a pathogenic yeast associated with systemic infections, exhibits metabolic adaptability in response to nutrient availability. Methods We investigated the impact of RPMI glucose supplemented (RPMId), TSB, BHI and YPD media on C. parapsilosis growth, morphology, susceptibility (caspofungin and amphotericin B), and in vivo virulence (Galleria mellonella) in planktonic and biofilm states. Results High-glucose media favors growth but hinders metabolic activity and filamentation. Media promoting carbohydrate production reduces biofilm susceptibility. Virulence differences between planktonic cells and biofilm suspensions from the same media shows that biofilm-related factors influence infection outcome depending on nutrient availability. Pseudohyphal growth occurred in biofilms under low oxygen and shear stress, but its presence is not exclusively correlated with virulence. Discussion This study provides valuable insights into the intricate interplay between nutrient availability and C. parapsilosis pathogenicity. It emphasizes the importance of considering pathogen behavior in diverse conditions when designing research protocols and therapeutic strategies.
Antibiotic Resistance Genes, Virulence Factors, and Biofilm Formation in Coagulase-Negative Staphylococcus spp. Isolates from European Hakes (Merluccius merluccius, L.) Caught in the Northeast Atlantic Ocean

The indiscriminate use of antibiotics has contributed to the dissemination of multiresistant bacteria, which represents a public health concern. The aim of this work was to characterize 27 coagulase-negative staphylococci (CoNS) isolated from eight wild Northeast Atlantic hakes (Merluccius merluccius, L.) and taxonomically identified as Staphylococcus epidermidis (n = 16), Staphylococcus saprophyticus (n = 4), Staphylococcus hominis (n = 3), Staphylococcus pasteuri (n = 2), Staphylococcus edaphicus (n = 1), and Staphylococcus capitis (n = 1). Biofilm formation was evaluated with a microtiter assay, antibiotic susceptibility testing was performed using the disk diffusion method, and antibiotic resistance and virulence determinants were detected by PCR. Our results showed that all staphylococci produced biofilms and that 92.6% of the isolates were resistant to at least one antibiotic, mainly penicillin (88.8%), fusidic acid (40.7%), and erythromycin (37%). The penicillin resistance gene (blaZ) was detected in 66.6% (18) of the isolates, of which 10 also carried resistance genes to macrolides and lincosamides (mphC, msr(A/B), lnuA, or vgaA), 4 to fusidic acid (fusB), and 3 to trimethoprim-sulfamethoxazole (dfrA). At least one virulence gene (scn, hla, SCCmecIII, and/or SCCmecV) was detected in 48% of the isolates. This study suggests that wild European hake destined for human consumption could act as a vector of CoNS carrying antibiotic resistance genes and/or virulence factors.
Wet coffee processing wastewater treatment by using an integrated constructed wetland

A wet coffee processing plant is an agro-industry that generates huge volumes of medium to high-strength wastewater that needs proper treatment before being released into the environment. Low-income countries must adopt an integrated, easily adaptable, and eco-friendly system to treat such effluent. The objective of this study was to treat wet coffee processing wastewater (WCPWW) using pretreatment units (aeration and sedimentation) and a macrosom scale HSSFCW cells, each 1.80 m × 0.60 m × 0.50 m (length × width × depth; area = 1.08 m 2 ) planted with emergent wetland plants. Three HSSFCW cells whose bottom and sides get lined with plastic membranes were filled with gravel and planted with the wetland plants ( Cyperus alternifolius , Vetiveria zizanioides , and Pennisetum purpureum ), while the fourth cell was left unplanted (control). The HSSFCW cells were fed with different tap water and WCPWW mix ratios at the 7 d interval until the plants adapted to the new environment. After pretreated and pH adjusted to 6.10, the WCPWW was allowed to enter the HSSFCW cells from an equalization tank via plastic pipes equipped with control valves. Triplicate samples were collected from the inlets and outlets of each treatment unit and analyzed in the laboratory according to standard methods. The results revealed that sedimentation and aeration units achieved 51.80 and 19.80 for BOD 5 , 61.60 and 22.10 for COD, –46.70 and 26.50 for NO 3– –N, 17.0 and 38.50 for NH 3 –N, 19.10 and 8.10 for PO 43– –P, 76.10 and 19.60 for TSS, 50.90 and 27.50 for TDS and –23.30 and 27.70 for EC % removals, respectively. HSSFCW 2 , (planted with V. zizanioides ) and HSSFCW 3 (control) cells achieved 78.50 and 61.70 for BOD 5 , 80.10 and 69.10 for COD, 70.20 and 43.20 for NO 3– –N, 50.10 and 29.0 for NH 3 –N, 79.60 and 57.40 for PO 43– –P, 72.40 and 65.80 for TSS and 51.20 and 42.80 for TDS, and 31.10 and 22.30 for EC % removal respectively. The wetland cell, HSSFCW 2 achieved a better % removal for organic matter, solids, and nutrients. In conclusion, the integrated system is a good option for treating WCPWW. The treatment system must integrate more units to achieve effluent compliance with discharge limits.
The statistical emulators of GGCMI phase 2: responses of year-to-year variation of crop yield to CO2, temperature, water, and nitrogen perturbations

Abstract. Understanding the impact of climate change on year-to-year variation of crop yield is critical to global food stability and security. While crop model emulators are believed to be lightweight tools to replace the models, few emulators have been developed to capture such interannual variation of crop yield in response to climate variability. In this study, we developed a statistical emulator with a machine learning algorithm to reproduce the response of year-to-year variation of four crop yields to CO2 (C), temperature (T), water (W), and nitrogen (N) perturbations defined in the Global Gridded Crop Model Intercomparison Project (GGCMI) phase 2. The emulators were able to explain more than 52 % of the variance of simulated yield and performed well in capturing the year-to-year variation of global average and gridded crop yield over current croplands in the baseline. With the changes in CO2–temperature–water–nitrogen (CTWN) perturbations, the emulators could reproduce the year-to-year variation of crop yield well over most current cropland. The variation of R and the mean absolute error was small under the single CTWN perturbations and dual-factor perturbations. These emulators thus provide statistical response surfaces of yield, including both its mean and interannual variability, to climate factors. They could facilitate spatiotemporal downscaling of crop model simulation, projecting the changes in crop yield variability in the future and serving as a lightweight tool for multi-model ensemble simulation. The emulators enhanced the flexibility of crop yield estimates and expanded the application of large-ensemble simulations of crop yield under climate change.
A Protocol and database for monitoring transient multi-species reef fish apawning aggregations in the Meso-American Reef

Most commercially important Caribbean reef fish species reproduce within transient spawning aggregations in specific times and places. Fishers have long recognized and capitalized on this behavior, and heavy fishing pressure on spawning aggregations has led to declines and extirpations around the Caribbean, particularly for Nassau grouper. For the same reason that spawning aggregations are attractive to fishers, they are also an opportunity for managers to monitor the populations. To maximize this opportunity, we developed, tested, and produced a standardized protocol and accompanying database for monitoring transient reef fish spawning aggregations. The protocol includes both fisheries dependent and independent techniques for data collection as well as physical oceanographic measures. The accompanying database and user manual are designed intimately with the monitoring protocol, providing easy data entry and data retrieval via generation of reports. The system design allows upgrading to a web-based, SQL-server platform that can handle data from around the world. The protocol has been adopted by the World Bank’s Meso-American Barrier Reef Systems Project (MBRS) for Belize, Mexico, Honduras and Guatemala.