Miracle-dz/UniFAR-FTUs huggingface dataset:
Rice Diseases Recognition Using Effective Deep Learning Models

Rice is the most important grain in Thailand for both consuming and exporting. One of the critical problems in rice cultivation is rice diseases, which affects directly to the yield. Disease recognition by a human is hard and the performance depends on the farmer’s experience. To overcome this problem, we did two folds of contributions. First, an infield rice disease image dataset was created. Second, a number of deep learning models including ResNets and DenseNets were applied to classify such rice diseases. The experimental results reveal that the proposed framework can achieve high accuracy, more than 95% in average, and has potential to be implemented and provide to Thai farmers in the future.
The relationship between quality and outcomes in routine depression care.

OBJECTIVE This longitudinal, nonexperimental study examined whether depression treatment provided in concordance with guidelines developed by the Agency for Healthcare Research and Quality (AHRQ) is associated with improved clinical outcomes. METHODS The medical, insurance, and pharmacy records of a community-based sample of 435 subjects who screened positive for current major depression were abstracted to ascertain whether depression treatment was received and whether it was provided in accordance with AHRQ guidelines. Regression analyses estimated the impact of guideline-concordant treatment on the change in depression severity and on mental and physical health over a six-month period. An instrumental variables analysis was used to check the sensitivity of the results to selection bias. RESULTS A total of 106 subjects were treated for depression by 105 different primary care and specialty providers. Sixty percent of the sample had current major depression, and about 40 percent had subthreshold depression. Only 29 percent of the patients received guideline-concordant treatment. For patients with major depression, guideline-concordant care was significantly and substantially associated with improved depression severity but not with improvements in overall mental or physical health. The instrumental variables analysis indicated that the standard regression analysis underestimated the treatment effect by 21 percent. For those with subthreshold depression, guideline-concordant care was not associated with improved outcomes. DISCUSSION AND CONCLUSIONS This community-based, nonexperimental study found a positive relationship between the quality of care for depression and clinical outcomes for patients with major depression in routine practice settings.
Serum matrix metalloproteinases MMP-2 and MMP-9 and metalloproteinase tissue inhibitors TIMP-1 and TIMP-2 in diabetic nephropathy.

BACKGROUND The regulation of mesangial extracellular matrix (ECM) turnover engages a number of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). High glucose concentration affects ECM degradation and the activities of MMPs and TIMPs. ECM accumulation is involved in the pathogenesis of diabetic nephropathy. METHODS Serum MMP-9, MMP-2, TIMP-2 and TIMP-1 were measured with ELISA in patients with either chronic renal failure (CRF, n=20), type 2 diabetes mellitus (DM2, n=16) or diabetic nephropathy (DM2+CRF, n=14), and healthy controls (n=20). RESULTS Diabetic nephropathy was related with profound decrease of serum TIMP-2 (122.2 +/- 47.2 vs. 263.0 +/- 89.2 ng/mL), TIMP-1 (242.5 +/- 96.9 vs. 347.4 +/- 87.2 ng/mL) and MMP-2 (385.4 +/- 42.6 vs. 517.2 +/- 75.4 ng/mL) (p<0.001). Both TIMP-1 and TIMP-2 were reduced in diabetic nephropathy in comparison with either diabetes alone (p<0.01 and p<0.001; respectively) or CRF alone (p<0.001 for both). An approximately 2-fold increase of MMP-9/TIMP-1 and MMP-2/TIMP-2 ratio was found in diabetic nephropathy when compared with diabetes with normal renal function (p<0.01). Further, in DM2 patients, TIMP-2 was decreased when compared with CRF alone (219.2 +/- 71.8 vs. 296.8 +/- 58.4 ng/mL). MMP-2 was lowered in both groups of DM2 and CRF patients (413.8 +/- 59.0 ng/mL and 409.7 +/- 93.1 ng/mL, vs. normal control value of 517.2 +/- 75.4 ng/mL; p<0.001). CONCLUSIONS These data indicate that circulating TIMP-1, TIMP-2 and MMP-2 are decreased in patients with diabetic nephropathy when compared with either CRF or diabetes.
Transient expression of human adenosine deaminase cDNAs: identification of a nonfunctional clone resulting from a single amino acid substitution

Human adenosine deaminase (ADA) is an important purine catabolic enzyme which irreversibly deaminates adenosine and deoxyadenosine. Severe genetic deficiency of ADA leads to an immunological deficiency state in which T-lymphoid cells are selectively destroyed by the accumulation of toxic levels of deoxyadenosine and deoxy-ATP. In preparation for transfer of ADA sequences into a variety of cell types, we explored expression of ADA cDNAs transfected into cultured cells within a simian virus 40-based expression vector. After transfection into monkey kidney (COS) cells, ADA cDNA encompassing the entire coding region of the protein generated human ADA activity. An unexpected finding, however, was the identification of a cDNA clone that failed to produce either human enzyme activity or immunoreactive ADA protein. As this pattern is typical of many naturally occurring mutant ADA alleles, we characterized the molecular defect in this clone. DNA sequence analysis revealed a single nucleotide substitution in amino acid position 50 (glycine-valine). Northern blotting with a unique 17-mer oligonucleotide demonstrated the absence of the mutant sequence in the mRNA from which the cDNA library giving rise to the mutant cDNA was constructed. Therefore, the substitution in the variant cDNA was created during cloning. These data define one critical region of the human ADA protein molecule and suggest a convenient strategy for characterization of the phenotypes associated with naturally occurring mutant alleles.
Gene Expression Signature of the Gross Morphology in Hepatocellular Carcinoma

Objective:To evaluate the gene expression signature of hepatocellular carcinoma (HCC) in relation to the gross morphology. Background:Eggel's nodular type of HCC is morphologically subclassified into the single nodular (SN) type, the single nodular type with extranodular growth (SNEG), and the confluent multinodular (CM) type, but their biomolecular differences remain unclear. Methods:The clinicopathological characteristics and genome-wide gene expressions were analyzed in 275 patients with nodular-type HCC (124 SN-type, 91 SNEG-type, and 60 CM-type) who received curative hepatectomy. Results:Significantly poor prognosis was recognized in CM types in overall survival (P = 0.0020) and recurrence-free survival (P = 0.0066). Analysis of the genome-wide expression patterns revealed significant difference of CM-type HCC from either SN- or SNEG-type HCC. In particular, a stem cell marker EpCAM was dominantly expressed in CM-type HCC. Immunohistochemical studies confirmed the specific expression of EpCAM in HCC cancer cells of CM type. In multivariate analysis, the gross morphology of CM type was significantly associated with EpCAM expression (P = 0.0092), &agr;-fetoprotein (P = 0.0424), “lens culinaris agglutinin-reactive fraction of &agr;-fetoprotein” level (P = 0.0288), and the portal vein invasion (P = 0.0150). Furthermore, EpCAM was predictive for poor prognosis in overall and recurrence-free survivals of patients with CM-type HCC (P = 0.0082 and P = 0.0043, respectively). Conclusion:Our studies suggest that the distinct signature of gene expression is closely related to morphological progression in HCC. Especially, EpCAM might play a critical role in the aggressiveness of CM-type HCC.
Acute Impact of Volcanic Ash on Asthma Symptoms and Treatment

Information about the impacts of disasters on health is useful for establishing hazard prediction maps and action plans of disaster management. This study aims at learning effective asthma management from the volcano disaster of Mount Asama eruption in Japan on September 1, 2004. We conducted a cross-sectional study to assess the acute impact of volcanic ash on asthma symptoms and their treatment changes by using a questionnaire completed by 236 adult asthmatic patients and their physicians. In the ashfall over 100g/m2 area, 42.9% of asthma patients suffered exacerbations, PEF decreased, asthma treatments increased, and inhalation of β2 stimulants was used most for exacerbated asthma. Compared to severe asthma patients, mild and moderate asthma patients were most at risk. Severe asthma patients were not affected since most of them knew their asthma status was severe, and did not go outside and kept windows closed. Deteriorated asthma symptoms of wheezing, chest tightness and cough appeared in the ashfall over 100g/m2 area. Ash contained inhalable 10μm diameter particles, and included high concentrations of airway toxic substrates of silica. These data suggest that ashfall over 100 g/m2 is harmful, access to these areas by asthma patients needs to be restricted, and these areas need to improve asthma treatment. In addition, the increase in the proportion of asthma patients with wheeze and cough are diagnostic clues for ash-induced asthma in affected areas, and can be used by doctors to tell whether patients are receiving sufficient asthma treatment.
A Neuro-VR toolbox for assessment and intervention in Autism: Brain responses to non-verbal, gaze and proxemics behaviour in Virtual Humans.

This research plans to investigate non-verbal social interaction in a virtual environment. Participants are required to interact with a virtual human (VH) in order to complete a puzzle using only eye-gaze. The project will focus on joint attention (JA) that can be categorised into two processes, initiation (IJA) and response (RJA). Firstly, we will investigate these categories by recording behaviours such as accuracy, completion times and the participants’ eye-tracking data to influence JA behaviour of the VH. This will later progress to investigate neural substrates using electrophysiological recordings of the brain (EEG). Based on previous research [1; 5], we expect differences to manifest in the neural signatures that are representative of each process. Manipulations will centre around the proximity of the character and the use of distractions; objects randomly appearing in the scene, eliciting overt and sometimes, covert gaze responses. The final stage of the project will incorporate a closed-loop system that is moderated by the EEG signals. This, in turn, will modulate the behaviour of the VH i.e. the proximity and/or extent of cooperation throughout the task.
Emotional signals in nonverbal interaction: Dyadic facilitation and convergence in expressions, appraisals, and feelings

We examined social facilitation and emotional convergence in amusement, sadness, and fear in dynamic interactions. Dyads of friends or strangers jointly watched emotion-eliciting films while they either could or could not communicate nonverbally. We assessed three components of each emotion (expressions, appraisals, and feelings), as well as attention to and social motives toward the co-participant. In Study 1, participants interacted through a mute videoconference. In Study 2, they sat next to each other and either were or were not separated by a partition. Results revealed that facilitation and convergence are not uniform across different emotions and emotion components. Particularly strong supporting patterns emerged for the facilitation of and convergence in smiling. When direct interaction was possible (Study 2), friends showed a general tendency for strong convergence, with the exception of fear-related appraisals. This suggests that underlying processes of emotional contagion and social appraisal are differentially relevant for different emotions.
Biliary secretion of anionic polypeptide fraction is not coupled to that of phospholipids and cholesterol in rats

Anionic polypeptide fraction (APF) is a phospholipid‐ and calcium‐binding apoprotein present in animal and human bile, predominantly associated with cholesterol‐phospholipid vesicles. In bile, the protein may play a physiological role in preventing precipitation of calcium salts. APF has also been suggested to be of regulatory importance in the process of biliary lipid secretion. The aim of the present study was to investigate whether the secretion rates of APF and that of biliary lipids are coupled, which would support a physiological role of APF in biliary lipid secretion. Biliary secretion rates of bile acids, phospholipids, and cholesterol were experimentally modulated in three different rat models. Secretion rates of APF were compared with that of bile acids, lipids, and with that of two other biliary proteins, the lysosomal protein β‐glucuronidase and apolipoprotein A‐I (apo A‐I). Model 1: diurnal variation in bile formation during chronic bile diversion; model 2: specific inhibition of biliary phospholipid and cholesterol, but not of bile acid secretion by infusion of the organic anion, sulfated lithocholyltaurine; model 3: acute interruption of the enterohepatic circulation in unanesthetized rats. The diurnal variation in bile formation involved a parallel increase of the biliary secretion rates of bile acids (+56 ± 7%, mean ± SD), phospholipids (+53 ± 29%), cholesterol (+73 ± 54%), and APF (+72 ± 86%) during the night phase of the cycle. Infusion of sulfated lithocholyltaurine inhibited biliary phospholipid and cholesterol secretion (−78 ± 15%, and −54 ± 25%, respectively), but did not affect biliary bile acid or APF secretion rate (−19 ± 14%, and +12 ± 107%, respectively). Within 4 hours after interruption of the enterohepatic circulation, bile secretion rates for bile acids (−92 ± 3%), phospholipids (−74 ± 13%), cholesterol (−64 ± 8%), and APF (−58 ± 24%) rapidly declined to a new steady‐state level. Correlation analysis using the data from the three experimental models indicated that the biliary secretion rate of APF was independent from that of phospholipids, cholesterol, β‐glucuronidase, and, presumably, apolipoprotein A‐I, and positively correlated to bile acid secretion rate and bile flow. The data from three experimental models indicate that the biliary secretion rates of APF and of phospholipids/cholesterol are not coupled and, therefore, do not support a direct physiological role of APF secretion in biliary lipid secretion. APF secretion into bile may, at least partially, be controlled by biliary bile acid secretion.
Intravenous Administration of Propacetamol Reduces Morphine Consumption After Spinal Fusion Surgery

We sought to determine the analgesic efficacy, opioid-sparing effects, and tolerability of propacetamol, an injectable prodrug of acetaminophen, in combination with morphine administered by patient-controlled analgesia (PCA) after spinal fusion surgery. Forty-two patients undergoing spinal stabilization surgery were randomized into two groups, which were given either an IV placebo or an IV injection of 2 g propacetamol every 6 h for 3 days after surgery. The postoperative opioid analgesic requirement was assessed with a PCA device used to self-administer morphine. Pain relief was evaluated by a visual analog pain scale and by verbal rating scores of pain relief at 8-h intervals for up to 72 h after surgery. The cumulative dose of morphine at 72 h was smaller in the Propacetamol group than in the Placebo group (60.3 ± 20.5 vs 112.2 ± 39.1 mg;P < 0.001). The pain scores were significantly lower in the Propacetamol group measured at two intervals of the study, although visual analog scale pain intensity scores were smaller than 3 in both groups. Most patients in the Placebo group obtained a greater degree of sedation on postoperative Day 3 (P < 0.05). This study demonstrates the usefulness of propacetamol as an adjunct to PCA morphine in the treatment of postoperative pain after spinal fusion.
In vitro antibacterial activities of tigecycline in combination with other antimicrobial agents determined by chequerboard and time-kill kinetic analysis.

OBJECTIVES This study was undertaken to determine the interaction of tigecycline with 13 select antimicrobial agents against a wide variety of Gram-negative and Gram-positive bacterial isolates. METHODS Antibiotic interactions were assayed using the chequerboard MIC format and selected synergistic combinations were confirmed using time-kill kinetic analysis. RESULTS Microdilution chequerboard analysis of tigecycline in combination with amikacin, ampicillin/sulbactam, azithromycin, ciprofloxacin, colistin, imipenem, levofloxacin, piperacillin, piperacillin/tazobactam, polymyxin B, rifampicin, minocycline and vancomycin resulted in an interpretation of either no interaction or synergy. Time-kill kinetic analysis resulted in an interpretation of no interaction for all but one of the drug combinations that resulted in an interpretation of synergy by the chequerboard analysis. Antagonism was not observed for any combination when assayed by either method. CONCLUSIONS The lack of antagonism seen with tigecycline combinations in both chequerboard and time-kill kinetic studies is an encouraging outcome, suggesting that tigecycline may prove to be effective in combination therapy as well as in monotherapy.
Decreased AIRE Expression and Global Thymic Hypofunction in Down Syndrome

The Down syndrome (DS) immune phenotype is characterized by thymus hypotrophy, higher propensity to organ-specific autoimmune disorders, and higher susceptibility to infections, among other features. Considering that AIRE (autoimmune regulator) is located on 21q22.3, we analyzed protein and gene expression in surgically removed thymuses from 14 DS patients with congenital heart defects, who were compared with 42 age-matched controls with heart anomaly as an isolated malformation. Immunohistochemistry revealed 70.48 ± 49.59 AIRE-positive cells/mm2 in DS versus 154.70 ± 61.16 AIRE-positive cells/mm2 in controls (p < 0.0001), and quantitative PCR as well as DNA microarray data confirmed those results. The number of FOXP3-positive cells/mm2 was equivalent in both groups. Thymus transcriptome analysis showed 407 genes significantly hypoexpressed in DS, most of which were related, according to network transcriptional analysis (FunNet), to cell division and to immunity. Immune response-related genes included those involved in 1) Ag processing and presentation (HLA-DQB1, HLA-DRB3, CD1A, CD1B, CD1C, ERAP) and 2) thymic T cell differentiation (IL2RG, RAG2, CD3D, CD3E, PRDX2, CDK6) and selection (SH2D1A, CD74). It is noteworthy that relevant AIRE-partner genes, such as TOP2A, LAMNB1, and NUP93, were found hypoexpressed in DNA microarrays and quantitative real-time PCR analyses. These findings on global thymic hypofunction in DS revealed molecular mechanisms underlying DS immune phenotype and strongly suggest that DS immune abnormalities are present since early development, rather than being a consequence of precocious aging, as widely hypothesized. Thus, DS should be considered as a non-monogenic primary immunodeficiency.
Relationship between indoleamine 2,3-dioxygenase activity and lymphatic invasion propensity of colorectal carcinoma.

AIM To evaluate whether serum and tumor indoleamine 2,3-dioxygenase activities can predict lymphatic invasion (LI) or lymph node metastasis in colorectal carcinoma. METHODS The study group consisted of 44 colorectal carcinoma patients. The patients were re-grouped according to the presence or absence of LI and lymph node metastasis. Forty-three cancer-free subjects without any metabolic disturbances were included into the control group. Serum neopterin was measured by enzyme linked immunosorbent assay. Urinary neopterin and biopterin, serum tryptophan (Trp) and kynurenine (Kyn) concentrations of all patients were determined by high performance liquid chromatography. Kyn/Trp was calculated and its correlation with serum neopterin was determined to estimate the serum indoleamine 2,3-dioxygenase activity. Tissue sections from the studied tumors were re-examined histopathologically and were stained by immunohistochemistry with indoleamine-2,3-dioxygenase antibodies. RESULTS Neither serum nor urinary neopterin was significantly different between the patient and control groups (both P > 0.05). However, colorectal carcinoma patients showed a significant positive correlation between the serum neopterin levels and Kyn/Trp (r = 0.450, P < 0.01). Urinary biopterin was significantly higher in cancer cases (P < 0.05). Serum Kyn/Trp was significantly higher in colorectal carcinoma patients (P < 0.01). Lymphatic invasion was present in 23 of 44 patients, of which only 12 patients had lymph node metastasis. Eleven patients with LI had no lymph node metastasis. Indoleamine-2,3-dioxygenase intensity score was significantly higher in LI positive cancer group (44.56% ± 6.11%) than negative colorectal cancer patients (24.04% ± 6.90%), (P < 0.05). Indoleamine 2,3-dioxygenase expression correlated both with the presence of LI and lymph node metastasis (P < 0.01 and P < 0.05, respectively). A significant difference between the accuracy of diagnosis by using either total indoleamine-2,3-dioxygenase immunostaining score or of lymph node metastasis was found during the evaluation of cancer patients. CONCLUSION Indoleamine-2,3-dioxygenase expression may predict the presence of unrecognized LI and lymph node metastasis and may be included in the histopathological evaluation of colorectal carcinoma cases.
Family of Kunitz proteins from trophoblast: Expression of the trophoblast Kunitz domain proteins (TKDP) in cattle and sheep

Here we report the molecular cloning of several members of a family of novel proteins expressed by the ruminant trophoblast, known as the trophoblast Kunitz domain proteins (TKDPs). Each contains a carboxyl‐terminal module of ∼64 amino acids belonging to the Kunitz family of serine proteinase inhibitors. These Kunitz modules are preceded by one or more structurally related domains, each about 80 amino acids long. The function of these domains is unclear. The TKDPs differ considerably in sequence identity, with much of the diversity due to variability in the amino‐terminal domains. However, nine of the ten Kunitz domains described here are themselves unique, ranging in amino acid sequence identity from 90% to 53% to each other and averaging only about 50% identity with bovine pancreatic trypsin inhibitor (BPTI). The “warhead” P1 residues, which govern specificity, are themselves variable and include some unusual amino acids, such as Asn, Thr, and Ile, as well as the more common Lys. The Kunitz domains of three of the TKDPs lack the conserved cysteines at positions 14 and 38 (BPTI numbering) that normally contribute to the orientation of the inhibitory loop. Northern blotting and reverse transcription‐polymerase chain reaction (RT‐PCR) demonstrated that the TKDP genes do not exhibit identical expression patterns during trophoblast development, although mostly are expressed maximally during early pregnancy. It is possible that the TKDPs provide a broad range of specificities against maternal proteinases that might be damaging to the trophoblast during pregnancy. Mol. Reprod. Dev. 65: 30–40, 2003. © 2003 Wiley‐Liss, Inc.