Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding Complex Biological Relationships in Recent PubMed Articles Using Bio-LDA

The overwhelming amount of available scholarly literature in the life sciences poses significant challenges to scientists wishing to keep up with important developments related to their research, but also provides a useful resource for the discovery of recent information concerning genes, diseases, compounds and the interactions between them. In this paper, we describe an algorithm called Bio-LDA that uses extracted biological terminology to automatically identify latent topics, and provides a variety of measures to uncover putative relations among topics and bio-terms. Relationships identified using those approaches are combined with existing data in life science datasets to provide additional insight. Three case studies demonstrate the utility of the Bio-LDA model, including association predication, association search and connectivity map generation. This combined approach offers new opportunities for knowledge discovery in many areas of biology including target identification, lead hopping and drug repurposing.
Trajectory and heading tracking of a mecanum wheeled robot using fuzzy logic control

This paper presents trajectory tracking and heading adjustment systems of a Mecanum wheel robot using fuzzy logic controller (FLC) and inertia measurement unit (IMU) sensor. It is known that when a Mecanum wheel robot moves, its wheels may slip due to various floor conditions. During such a slip condition, the exact position and orientation of the robot often deviate from that which was intended. In order to reduce the size of this deviation, the Mecanum wheel was equipped with an IMU sensor which measures the orientation (heading) of the Mecanum wheel robot. The implementation of the IMU sensor as a heading sensor usually achieved using a complementary filterThe FLC, on the other hand, is used to force the Mecanum wheel robot to follow a given trajectory with minimum heading deviation. As a result, the FLC system and the IMU sensor provide a robust navigation scheme for Mecanum wheel robot without the need for external references such as beacons or visual markers. The implementation of our approach on the Mecanum wheel robot was achieved using embedded microcontroller for motion control and information acquisition. The developed FLC system was also deployed with a friendly graphical user interface which allows for the adjustment of fuzzification methods.
The Epidemiology and Clinical Spectrum of Melioidosis: 540 Cases from the 20 Year Darwin Prospective Study

Background Over 20 years, from October 1989, the Darwin prospective melioidosis study has documented 540 cases from tropical Australia, providing new insights into epidemiology and the clinical spectrum. Principal Findings The principal presentation was pneumonia in 278 (51%), genitourinary infection in 76 (14%), skin infection in 68 (13%), bacteremia without evident focus in 59 (11%), septic arthritis/osteomyelitis in 20 (4%) and neurological melioidosis in 14 (3%). 298 (55%) were bacteremic and 116 (21%) developed septic shock (58 fatal). Internal organ abscesses and secondary foci in lungs and/or joints were common. Prostatic abscesses occurred in 76 (20% of 372 males). 96 (18%) had occupational exposure to Burkholderia pseudomallei. 118 (22%) had a specific recreational or occupational incident considered the likely infecting event. 436 (81%) presented during the monsoonal wet season. The higher proportion with pneumonia in December to February supports the hypothesis of infection by inhalation during severe weather events. Recurrent melioidosis occurred in 29, mostly attributed to poor adherence to therapy. Mortality decreased from 30% in the first 5 years to 9% in the last five years (p<0.001). Risk factors for melioidosis included diabetes (39%), hazardous alcohol use (39%), chronic lung disease (26%) and chronic renal disease (12%). There was no identifiable risk factor in 20%. Of the 77 fatal cases (14%), 75 had at least one risk factor; the other 2 were elderly. On multivariate analysis of risk factors, age, location and season, the only independent predictors of mortality were the presence of at least one risk factor (OR 9.4; 95% CI 2.3–39) and age ≥50 years (OR 2.0; 95% CI 1.2–2.3). Conclusions Melioidosis should be seen as an opportunistic infection that is unlikely to kill a healthy person, provided infection is diagnosed early and resources are available to provide appropriate antibiotics and critical care.
Technological trends and market perspectives for production of microbial oils rich in omega-3

Abstract In recent years, foods that contain omega-3 lipids have emerged as important promoters of human health. These lipids are essential for the functional development of the brain and retina, and reduction of the risk of cardiovascular and Alzheimer's diseases. The global market for omega-3 production, particularly docosahexaenoic acid (DHA), saw a large expansion in the last decade due to the increasing use of this lipid as an important component of infant food formulae and supplements. The production of omega-3 lipids from fish and vegetable oil sources has some drawbacks, such as complex purification procedures, unwanted contamination by marine pollutants, reduction or even extinction of several species of fish, and aspects related to sustainability. A promising alternative system for the production of omega-3 lipids is from microbial metabolism of yeast, fungi, or microalgae. The aim of this review is to discuss the various omega-3 sources in the context of the global demand and market potential for these bioactive compounds. To summarize, it is clear that fish and vegetable oil sources will not be sufficient to meet the future needs of the world population. The biotechnological production of single-cell oil comes as a sustainable alternative capable of supplementing the global demand for omega-3, causing less environmental impact.
STRATEGI REGULASI EMOSI DAN POLA ASUH ORANG TUA MELATARBELAKANGI PERILAKU BINGE EATING PADA REMAJA

ABSTRAK Penelitian mengenai binge eating belum banyak dilakukan di Indonesia. Binge eating adalah perilaku makan berlebihan yang merupakan salah satu mental disorder utama pada remaja, khususnya pada remaja yang berusia 15–19 tahun. Tujuan: Melihat hubungan strategi regulasi emosi dan pola asuh orang tua dengan perilaku binge eating pada remaja usia 15–19 tahun di DKI Jakarta. Metode: Penelitian ini merupakan penelitian kuantitatif jenis observasional analitik dengan desain penelitian cross sectional dan menggunakan uji statistik nonparametrik, yaitu uji chi-square . Sampel pada penelitian ini berjumlah 388 remaja yang memenuhi kriteria inklusi dan didapatkan melalui teknik probability sampling jenis cluster sampling . Sesuai dengan variabel-variabel yang ada, instrumen yang digunakan ialah instrumen karakteristik responden, Binge Eating Scale (BES), Emotion Regulation Questionnaire (ERQ), dan Parental Authority Questionnaire (PAQ). Hasil: Ditemukan sebesar 11% dari 388 remaja memiliki perilaku severe binge eating. Menggunakan uji chi-square, penelitian menunjukkan adanya hubungan yang signifikan antara strategi regulasi emosi dan
Modulation of Pancreatic Acinar Cell to Cell Coupling during ACh-evoked Changes in Cytosolic Ca2+ *

The temporal changes in cytosolic free Ca2+ ([Ca2+] i ), Ca2+-dependent membrane currents (Im ), and gap junctional current (Ij ) elicited by acetylcholine (ACh) were measured in rat pancreatic acinar cells using digital imaging and dual perforated patch-clamp recording. ACh (50 nm-5 μm) increased [Ca2+] i and evokedIm currents without alteringIj in 19 of 37 acinar cell pairs. Although [Ca2+] i rose asynchronously in cells comprising a cluster, the delay of the [Ca2+] i responses decreased with increasing ACh concentrations. Perfusion of inositol 1,4,5-trisphosphate (IP3) into one cell of a cluster resulted in [Ca2+] i responses in neighboring cells that were not necessarily in direct contact with the stimulated one. This suggests that extensive coupling between acinar cells provides a pathway for cell-to-cell diffusion of Ca2+-releasing signals. Strikingly, maximal (1–5 μm) ACh concentrations reduced Ij by 69 ± 15% (n = 9) in 25% of the cell pairs subjected to dual patch-clamping. This decrease occurred shortly after the Im peak and was prevented by incubating acinar cells in a Ca2+-free medium, suggesting that uncoupling was subsequent to the initiation of the Ca2+-mobilizing responses. Depletion of Ca2+-sequestering stores by thapsigargin resulted in a reduction of intercellular communication similar to that observed with ACh. In addition, ACh-induced uncoupling was prevented by blocking nitric oxide production with l-nitro-arginine and restored by exposing acinar cells to dibutyryl cGMP. The results suggest that ACh-induced uncoupling and capacitative Ca2+ entry are regulated concurrently. Closure of gap junction channels may occur to functionally isolate nearby cells differing in their intrinsic sensitivity to ACh and thereby to allow for sustained activity of groups of secreting cells.
Developmental basis of sexually dimorphic digit ratios

Males and females generally have different finger proportions. In males, digit 2 is shorter than digit 4, but in females digit 2 is the same length or longer than digit 4. The second- to fourth-digit (2D:4D) ratio correlates with numerous sexually dimorphic behavioral and physiological conditions. Although correlational studies suggest that digit ratios reflect prenatal exposure to androgen, the developmental mechanism underlying sexually dimorphic digit development remains unknown. Here we report that the 2D:4D ratio in mice is controlled by the balance of androgen to estrogen signaling during a narrow window of digit development. Androgen receptor (AR) and estrogen receptor α (ER-α) activity is higher in digit 4 than in digit 2. Inactivation of AR decreases growth of digit 4, which causes a higher 2D:4D ratio, whereas inactivation of ER-α increases growth of digit 4, which leads to a lower 2D:4D ratio. We also show that addition of androgen has the same effect as inactivation of ER and that addition of estrogen mimics the reduction of AR. Androgen and estrogen differentially regulate the network of genes that controls chondrocyte proliferation, leading to differential growth of digit 4 in males and females. These studies identify previously undescribed molecular dimorphisms between male and female limb buds and provide experimental evidence that the digit ratio is a lifelong signature of prenatal hormonal exposure. Our results also suggest that the 2D:4D ratio can serve as an indicator of disrupted endocrine signaling during early development, which may aid in the identification of fetal origins of adult diseases.
TDR analysis in the design of X-band LTCC tile T/R modules

Time Domain Reflectometry (TDR) has been introduced into the design of X-band tile Transmit/Receive (T/R) modules fabricated with Low Temperature Co-fired Ceramics (LTCC) processing. TDR simulation exhibits additional capability compared with S-parameter simulation, especially in the aspect of vertical interconnection scheme. Vertical quasi-coax interconnection and wire bonding schemes have been explored using TDR. Benefits brought from TDR made it an indispensable tool in designing compact tile T/R modules.
Host-induced gene silencing of cytochrome P450 lanosterol C14α-demethylase–encoding genes confers strong resistance to Fusarium species

Significance We demonstrate that host-induced gene silencing (HIGS) targeting the fungal sterol 14α-demethylase (CYP51) genes restricts Fusarium infection in plants. Fusarium diseases have a significant impact not only on global grain production, but also on food safety because of grain contamination with mycotoxins. We capitalized on the knowledge that demethylation inhibitor fungicides target cytochrome P450 lanosterol C-14α-demethylase. In Fusarium graminearum (Fg), this enzyme is encoded by three paralogous genes. Transgenic Arabidopsis and barley expressing a double-stranded RNA targeting all three CYP51 genes exhibited complete immunity to Fg. Our results provide proof-of-concept that HIGS of the CYP51 genes is an effective strategy for controlling Fusarium, demonstrating that HIGS is a powerful tool, which could revolutionize crop plant protection. Head blight, which is caused by mycotoxin-producing fungi of the genus Fusarium, is an economically important crop disease. We assessed the potential of host-induced gene silencing targeting the fungal cytochrome P450 lanosterol C-14α-demethylase (CYP51) genes, which are essential for ergosterol biosynthesis, to restrict fungal infection. In axenic cultures of Fusarium graminearum, in vitro feeding of CYP3RNA, a 791-nt double-stranded (ds)RNA complementary to CYP51A, CYP51B, and CYP51C, resulted in growth inhibition [half-maximum growth inhibition (IC50) = 1.2 nM] as well as altered fungal morphology, similar to that observed after treatment with the azole fungicide tebuconazole, for which the CYP51 enzyme is a target. Expression of the same dsRNA in Arabidopsis and barley rendered susceptible plants highly resistant to fungal infection. Microscopic analysis revealed that mycelium formation on CYP3RNA-expressing leaves was restricted to the inoculation sites, and that inoculated barley caryopses were virtually free of fungal hyphae. This inhibition of fungal growth correlated with in planta production of siRNAs corresponding to the targeted CYP51 sequences, as well as highly efficient silencing of the fungal CYP51 genes. The high efficiency of fungal inhibition suggests that host-induced gene-silencing targeting of the CYP51 genes is an alternative to chemical treatments for the control of devastating fungal diseases.
Prostate cancer and the unfolded protein response

The endoplasmic reticulum (ER) is an essential organelle that contributes to several key cellular functions, including lipogenesis, gluconeogenesis, calcium storage, and organelle biogenesis. The ER also serves as the major site for protein folding and trafficking, especially in specialized secretory cells. Accumulation of misfolded proteins and failure of ER adaptive capacity activates the unfolded protein response (UPR) which has been implicated in several chronic diseases, including cancer. A number of recent studies have implicated UPR in prostate cancer (PCa) and greatly expanded our understanding of this key stress signaling pathway and its regulation in PCa. Here we summarize these developments and discuss their potential therapeutic implications.
Clinical effect of neutralizing antibodies to interferon beta that persist long after cessation of therapy for multiple sclerosis.

OBJECTIVES To confirm that neutralizing antibodies (NAb) to interferon beta can persist after therapy withdrawal and to evaluate whether persisting NAb are associated with a worse clinical disease course in multiple sclerosis (MS). DESIGN Retrospective study. SETTING Tertiary referral center in The Netherlands. PATIENTS A total of 71 patients with relapsing-remitting multiple sclerosis treated with interferon beta in the past. MAIN OUTCOME MEASURES Persisting NAb after therapy withdrawal were tested using the cytopathic effect assay. Patients with and without persisting NAb were compared on several outcomes: the change in annualized relapse rate from prior to interferon beta treatment initiation to after cessation of treatment, time to sustained disability on the Kurtzke Expanded Disability Status Scale, and the use of disease-modifying treatments after cessation of treatment with interferon beta. RESULTS Seventeen of 71 patients (24%) tested NAb positive after a median interval of 25 months (interquartile range, 10-51 months) after interferon beta treatment cessation. Eleven of these 17 patients (15%) were high-titer NAb positive (>150 10-fold reduction units per mL). Persisting NAb were associated with an increase in the annualized relapse rate (P = .04) and a reduction in time to reach a sustained Expanded Disability Status Scale score of 6.0, ie, the need for unilateral assistance to walk 100 m (P = .02). Moreover, NAb-positive patients were treated with second-line therapy significantly more often, especially mitoxantrone (P = .006). CONCLUSION Anti-interferon beta NAb can persist after interferon beta treatment withdrawal and are associated with overt clinical disease activity. This is made apparent by an increase in relapse rate and faster disability progression and is supported by the observed need for more aggressive therapy after interferon beta treatment cessation. Prospective studies are warranted to confirm these results.
Note on Nordhaus-Gaddum Problems for Colin de Verdière type Parameters

We establish the bounds $\frac 4 3 \le b_\nu \le b_\xi\le \sqrt 2$, where $b_\nu$ and $b_\xi$ are the Nordhaus-Gaddum sum upper bound multipliers, i.e., $\nu(G)+\nu(\overline{G})\le b_\nu |G|$ and $\xi(G)+\xi(\overline{G})\le b_\xi | G|$ for all graphs $G$, and $\nu$ and $\xi$ are Colin de Verdiere type graph parameters. The Nordhaus-Gaddum sum lower bound for $\nu$ and $\xi$ is conjectured to be $|G| - 2$, and if these parameters are replaced by the maximum nullity $M(G)$, this bound is called the Graph Complement Conjecture in the study of minimum rank/maximum nullity problems.
A Bayesian method for 3D macromolecular structure inference using class average images from single particle electron microscopy

MOTIVATION Electron cryo-microscopy can be used to infer 3D structures of large macromolecules with high resolution, but the large amounts of data captured necessitate the development of appropriate statistical models to describe the data generation process, and to perform structure inference. We present a new method for performing ab initio inference of the 3D structures of macromolecules from single particle electron cryo-microscopy experiments using class average images. RESULTS We demonstrate this algorithm on one phantom, one synthetic dataset and three real (experimental) datasets (ATP synthase, V-type ATPase and GroEL). Structures consistent with the known structures were inferred for all datasets. AVAILABILITY The software and source code for this method is available for download from our website: http://compbio.cs. toronto.edu/cryoem/.
Nonfatal work-related motor vehicle injuries treated in emergency departments in the United States, 1998-2002.

BACKGROUND Current data on nonfatal work-related motor vehicle injuries are limited and fragmented, often excluding government workers, self-employed workers, and workers on small farms. This study seeks to bridge the present data gap by providing a national profile of nonfatal work-related motor vehicle injuries across all industries and occupations. METHODS Study subjects were people who suffered nonfatal work-related motor vehicle injuries and were treated in a hospital emergency department in the United States. Subjects were identified from a stratified probability sample of emergency departments. National estimates and rates were computed. RESULTS From 1998 to 2002, the average annual rate of nonfatal work-related motor vehicle injuries was 7 injuries per 10,000 full-time equivalents. The rate was three times higher in men than in women. The rates were higher in workers 15-19 years of age and in workers 70 years or older. Justice, public order, and safety workers had the largest number of injuries, and taxicab service employees had the highest injury rate of all industries. Truck drivers had the largest number of injuries, and police and detectives, public service employees had the highest injury rate of all occupations. CONCLUSION Future efforts need to develop and enhance the use of surveillance information at the federal and state level for work-related nonfatal motor vehicle injuries. Prevention efforts need to address occupational motor vehicle safety for both commercial truck/bus drivers and workers who are not commercial drivers but who drive light motor vehicles on the job.
Retrospective evaluation of patients with vitamin B12 deficiency in the pediatrics outpatient clinic

Background/Aim: This study examines patients diagnosed with vitamin B12 deficiency in our department. Although rare, vitamin B12 deficiency is one of the causes of megaloblastic anemia, which can lead to negative outcomes in patients. We aim to promote earlier diagnosis to protect patients from these negative effects. Therefore, this study will contribute to raising awareness in the literature. Methods: Retrospectively, we included a total of 127 outpatient children, aged 0–18 years (0–215 months), who were diagnosed and treated for vitamin B12 deficiency at the Bagcilar Training and Research Hospital Child Health and Disease Clinic between October 2014 and February 2015. Results: Among the patients, 67 (53%) with vitamin B12 deficiency were female, while 60 (47%) were male, indicating a higher occurrence in girls. Vitamin B12 deficiency was most commonly observed in the age groups of 0-2 years and 12-17 years (adolescents). The mean vitamin B12 level was 168.1 (34.1) pg/mL, the mean hemoglobin level was 12 (1.9) g/dL, and the mean MCV (mean corpuscular volume) was 78.4 (8.1) fl. Anemia was observed in 38% of the patients, bicytopenia in 4%, neutropenia in 6%, thrombocytopenia in 9%, pancytopenia in 3%, and macrocytosis in 2%. Non-iron-deficient patients showed no difference in mean hemoglobin and RDW (red cell distribution width) when compared to iron-deficient patients. However, their B12 levels were lower. The prevalence of iron deficiency did not differ between girls and boys. Comparing patients with vitamin B12 levels lower than 150 pg/mL to those with higher levels, there were no significant differences in average Hb, MCV, and RDW. Conclusion: It should be noted that macrocytic anemia is not exclusive to vitamin B12 deficiency. Vitamin B12 deficiency can manifest as normocytic anemia and should not be overlooked in biochemical assessments. It is recommended to conduct nationwide and regional prevalence studies to evaluate vitamin B12 deficiency as a public health issue and to develop new solutions accordingly.