Takshan/R1 huggingface dataset:
Use of chitin and chitosan to produce new chitooligosaccharides by chitinase Chit42: enzymatic activity and structural basis of protein specificity.

BACKGROUND: Chitinases are ubiquitous enzymes that have gained a recent biotechnological attention due to their ability to transform biological waste from chitin into valued chito-oligomers with wide agricultural, industrial or medical applications. The biological activity of these molecules is related to their size and acetylation degree. Chitinase Chit42 from Trichoderma harzianum hydrolyses chitin oligomers with a minimal of three N-acetyl-D-glucosamine (GlcNAc) units. Gene chit42 was previously characterized, and according to its sequence, the encoded protein included in the structural Glycoside Hydrolase family GH18. RESULTS: Chit42 was expressed in Pichia pastoris using fed-batch fermentation to about 3 g/L. Protein heterologously expressed showed similar biochemical properties to those expressed by the natural producer (42 kDa, optima pH 5.5-6.5 and 30-40 °C). In addition to hydrolyse colloidal chitin, this enzyme released reducing sugars from commercial chitosan of different sizes and acetylation degrees. Chit42 hydrolysed colloidal chitin at least 10-times more efficiently (defined by the kcat/Km ratio) than any of the assayed chitosan. Production of partially acetylated chitooligosaccharides was confirmed in reaction mixtures using HPAEC-PAD chromatography and mass spectrometry. Masses corresponding to (D-glucosamine)1-8-GlcNAc were identified from the hydrolysis of different substrates. Crystals from Chit42 were grown and the 3D structure determined at 1.8 Å resolution, showing the expected folding described for other GH18 chitinases, and a characteristic groove shaped substrate-binding site, able to accommodate at least six sugar units. Detailed structural analysis allows depicting the features of the Chit42 specificity, and explains the chemical nature of the partially acetylated molecules obtained from analysed substrates. CONCLUSIONS: Chitinase Chit42 was expressed in a heterologous system to levels never before achieved. The enzyme produced small partially acetylated chitooligosaccharides, which have enormous biotechnological potential in medicine and food. Chit42 3D structure was characterized and analysed. Production and understanding of how the enzymes generating bioactive chito-oligomers work is essential for their biotechnological application, and paves the way for future work to take advantage of chitinolytic activities.
The first transcriptomes from field-collected individual whiteflies ( Bemisia tabaci, Hemiptera: Aleyrodidae):  a case study of the endosymbiont composition.

Background:Bemisia tabaci species ( B. tabaci), or whiteflies, are the world's most devastating insect pests. They cause billions of dollars (US) of damage each year, and are leaving farmers in the developing world food insecure. Currently, all publically available transcriptome data for B. tabaci are generated from pooled samples, which can lead to high heterozygosity and skewed representation of the genetic diversity. The ability to extract enough RNA from a single whitefly has remained elusive due to their small size and technological limitations. Methods: In this study, we optimised a single whitefly RNA extraction procedure, and sequenced the transcriptome of four individual adult Sub-Saharan Africa 1 (SSA1) B. tabaci. Transcriptome sequencing resulted in 39-42 million raw reads. De novo assembly of trimmed reads yielded between 65,000-162,000 Contigs across B. tabaci transcriptomes. Results: Bayesian phylogenetic analysis of mitochondrion cytochrome I oxidase (mtCOI) grouped the four whiteflies within the SSA1 clade. BLASTn searches on the four transcriptomes identified five endosymbionts; the primary endosymbiont Portieraaleyrodidarum and four secondary endosymbionts: Arsenophonus, Wolbachia, Rickettsia, and Cardinium spp. that were predominant across all four SSA1 B. tabaci samples with prevalence levels of between 54.1 to 75%. Amino acid alignments of the NusG gene of P. aleyrodidarum for the SSA1 B. tabaci transcriptomes of samples WF2 and WF2b revealed an eleven amino acid residue deletion that was absent in samples WF1 and WF2a. Comparison of the protein structure of the NusG protein from P. aleyrodidarum in SSA1 with known NusG structures showed the deletion resulted in a shorter D loop. Conclusions: The use of field-collected specimens means time and money will be saved in future studies using single whitefly transcriptomes in monitoring vector and viral interactions. Our method is applicable to any small organism where RNA quantity has limited transcriptome studies.
Antenatally diagnosed congenital diaphragmatic hernia in Singapore: a five-year series.

INTRODUCTION: We aimed to investigate the epidemiology, diagnosis, prognostication, follow-up care and outcomes of antenatally diagnosed congenital diaphragmatic hernia (CDH) in KK Women's and Children's Hospital (KKH), Singapore. The objective of this study was to identify trends in current practice, and evaluate and improve the management of CDH. METHODS: We retrospectively reviewed cases of antenatally diagnosed CDH from 2006 to 2010. RESULTS: A total of 22 cases of CDH were found, bringing its incidence in KKH to 3.6 per 10,000 live births. The mean gestational age at diagnosis was 22.7 weeks, with 14 (63.6%) cases diagnosed at < 22 weeks and 8 (36.4%) diagnosed at ≥ 22 weeks. All cases were left-sided - 15 (68.2%) were isolated CDH and 7 (31.8%) were associated with other anomalies. Of the 22 cases, counselling about the prognosis of pregnancy based on the lung-to-head ratio was provided in 9 (40.9%). Overall, 10 (45.5%) cases resulted in termination of pregnancy (TOP), 9 (40.9%) resulted in live birth and 1 (4.5%) in stillbirth; 2 (9.1%) cases were lost to follow-up prior to delivery. Of the 9 live births, 3 (33.3%) resulted in neonatal death. In the 10 births, 5 (50.0%) were delivered by normal vaginal delivery, 4 (40.0%) by emergency Caesarean section and 1 (10.0%) by elective Caesarean section. CONCLUSION: CDH is a challenging perinatal problem with a low overall survival rate. Almost half of the cases opt for TOP. The data in this study can help clinicians better undertake the task of adequately counselling parents with qualitative and quantitative prognostic factors, using an evidence-based approach.
The insulin-like growth factor I receptor/insulin receptor tyrosine kinase inhibitor PQIP exhibits enhanced antitumor effects in combination with chemotherapy against colorectal cancer models.

PURPOSE: There is growing evidence implicating the importance of the insulin-like growth factor (IGF) pathway in colorectal cancer based upon the results of population studies and preclinical experiments. However, the combination of an IGF-I receptor (IGF-IR) inhibitor with standard colorectal cancer chemotherapies has not yet been evaluated. In this study, we investigated the interaction between PQIP, the dual IGF-IR/insulin receptor tyrosine kinase inhibitor, and standard chemotherapies in colorectal cancer cell line models. EXPERIMENTAL DESIGN: The antiproliferative effects of PQIP, as a single agent and in combination with 5-fluorouracil, oxaliplatin, or SN38, were analyzed against four colorectal cancer cell lines. Downstream effector proteins, apoptosis, and cell cycle were also assessed in the combination of PQIP and SN-38. Lastly, the efficacy of OSI-906 (a derivative of PQIP) combined with irinotecan was further tested using a human colorectal cancer xenograft model. RESULTS: Treatment with the combination of PQIP and each of three chemotherapies resulted in an enhanced decrease in proliferation of all four colorectal cancer cell lines compared with single-agent treatment. This inhibition was not associated with a significant induction of apoptosis, but was accompanied by cell cycle arrest and changes in phosphorylation of Akt. Interestingly, antitumor activity between PQIP and SN-38 in vitro was also reflected in the human colorectal cancer xenograft model. CONCLUSIONS: Combination treatment with PQIP, the dual IGF-IR/insulin receptor tyrosine kinase inhibitor, and standard colorectal cancer chemotherapy resulted in enhanced antiproliferative effects against colorectal cancer cell line models, providing a scientific rationale for the testing of OSI-906 and standard colorectal cancer treatment regimens.
Novel hemotropic mycoplasmas are widespread and genetically diverse in vampire bats.

Bats (Order: Chiroptera) have been widely studied as reservoir hosts for viruses of concern for human and animal health. However, whether bats are equally competent hosts of non-viral pathogens such as bacteria remains an important open question. Here, we surveyed blood and saliva samples of vampire bats from Peru and Belize for hemotropic Mycoplasma spp. ( hemoplasmas), bacteria that can cause inapparent infection or anemia in hosts. 16S rRNA gene amplification of blood showed 67% (150/223) of common vampire bats (Desmodus rotundus) were infected by hemoplasmas. Sequencing of the 16S rRNA gene amplicons revealed three novel genotypes that were phylogenetically related but not identical to hemoplasmas described from other (non-vampire) bat species, rodents, humans, and non-human primates. Hemoplasma prevalence in vampire bats was highest in non-reproductive and young individuals, did not differ by country, and was relatively stable over time (i.e., endemic). Metagenomics from pooled D. rotundus saliva from Peru detected non-hemotropic Mycoplasma species and hemoplasma genotypes phylogenetically similar to those identified in blood, providing indirect evidence for potential direct transmission of hemoplasmas through biting or social contacts. This study demonstrates vampire bats host several novel hemoplasmas and sheds light on risk factors for infection and basic transmission routes. Given the high frequency of direct contacts that arise when vampire bats feed on humans, domestic animals, and wildlife, the potential of these bacteria to be transmitted between species should be investigated in future work.
Optimizing the detection of lung cancer patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements potentially suitable for ALK inhibitor treatment.

PURPOSE: Anaplastic lymphoma kinase (ALK) rearrangements, associated with sensitivity to an experimental ALK/MET inhibitor, occur in 3% to 5% of non-small cell lung cancers. Intratumoral fluorescence in situ hybridization (FISH) heterogeneity has been reported. We explored the heterogeneity basis, the requirements for accurately determining ALK FISH positivity, and the effect of enriching the tested population using clinical and molecular factors. EXPERIMENTAL DESIGN: Lung cancer patients were screened by ALK and MET FISH and for EGFR and KRAS mutations. RESULTS: Thirteen ALK-positive cases were identified from 73 screened patients. Gene copy number increases occurred together with classic rearrangements. All positive cases were adenocarcinomas, 12 were EGFR/KRAS wild-type, and 1 had a coexistent EGFR exon 20 mutation. No association with MET amplification occurred. ALK positivity was associated with <10-pack-year smoking status (P = 0.0004). Among adenocarcinomas, without KRAS or EGFR mutations, with <10-pack-year history, 44.8% of cases were ALK positive. ALK FISH positivity was heterogeneous, but mean values in tumor areas from ALK-positive patients (54% of cells; range, 22-87%) were significantly higher than in adjacent normal tissue or tumor/normal areas from ALK-negative patients (mean, 5-7%). Contiguous sliding field analyses showed diffuse heterogeneity without evidence of focal ALK rearrangements. One hundred percent sensitivity and specificity occurred when four or more fields (∼60 cells) were counted. CONCLUSIONS: Intratumoral ALK FISH heterogeneity reflects technique, not biology. The clinical activity of ALK/MET inhibitors in ALK-positive patients probably reflects ALK, but not MET, activity. Prescreening by histology, EGFR/KRAS mutations, and smoking status dramatically increases the ALK-positive hit rate compared with unselected series.
Effect of filgotinib, a selective JAK 1 inhibitor, with and without methotrexate in patients with rheumatoid arthritis: patient-reported outcomes.

BACKGROUND: The aim was to assess patient-reported outcomes (PROs) in patients with rheumatoid arthritis (RA) treated with filgotinib during two phase 2b, 24-week, randomized, placebo-controlled studies. METHODS: Patients with moderate-to-severe active RA and an inadequate response to methotrexate (MTX) were randomized to daily placebo or filgotinib 50 mg, 100 mg, or 200 mg as add-on therapy to MTX (NCT01888874) or as monotherapy (NCT01894516). At week 12, nonresponders receiving filgotinib 50 mg in both studies or placebo in the add-on study, and all patients receiving placebo as monotherapy, were re-assigned to filgotinib 100 mg. PROs were measured using the Health Assessment Questionnaire - Disability Index (HAQ-DI) including Patient Pain assessed by visual analog scale, and the Patient Global Assessment of Disease Activity (Patient Global), the Functional Assessment of Chronic Illness Therapy (FACIT)-Fatigue Scale (Version 4), and the 36-Item Short Form Health Survey (SF-36). RESULTS: At week 12, improvements in all PROs, apart from the SF-36 mental component in the add-on study, were statistically better with filgotinib than placebo; some improvements were noted as early as the first assessment time point (week 1 or week 4). Filgotinib improved HAQ-DI by 0.58-0.84 points, FACIT-Fatigue by 6.9-11.4 points, Patient Global by 25.2-35.6 mm, and Pain by 24.2-37.9 mm; scores were maintained or improved to week 24. Across all PROs, more patients achieved minimal clinically important differences and normative values with filgotinib 200 mg than placebo. Patients re-assigned to filgotinib 100 mg at week 12 experienced improvements in PROs between weeks 12 to 24. CONCLUSIONS: Filgotinib as MTX add-on therapy or as monotherapy demonstrated rapid and sustained (to 24 weeks) improvements in health-related quality of life and functional status in patients with active RA. TRIAL REGISTRATION: MTX add-on study: ClinicalTrials.gov , NCT01888874 . Registered on 28 June 2013. Monotherapy study: ClinicalTrials.gov , NCT01894516 . Registered on 10 July 2013.
[Isolated pancreatic neck rupture].

Fracture isolée de l'isthme du pancréas. AIM OF THE STUDY: Through four cases of pancreatic neck rupture, the study aim was to emphasize the advantages of an early laparotomy when there is a doubt about a canal disruption and the risks of a later surgical management. PATIENTS AND RESULTS: Four patients were operated on for a neck disruption of the pancreas due to blunt trauma. Two patients underwent laparotomy in the first 48 hours after a radiological exploration and underwent a left pancreatectomy with spleen preservation. There were no associated injuries, no lesions of acute pancreatitis. The two other patients were, at first, medically treated and developed an acute pancreatitis with pseudocyst. They underwent laparotomy, 7 and 10 days after the trauma because of pain and hyperthermia, and a conservative treatment by cystojejunostomy was performed in difficult conditions because of the acute pancreatitis. A late pancreatic pseudocyst (4 and 6 months) occurred in two patients. CONCLUSION: When pancreatic trauma occurs, an exploration with echography, scanner, endoscopic retrograde cholangiopancreatography or magnetic resonance cholangiopancreatography can suggest a neck disruption and a canal rupture. When the canal is safe, a drainage close to the pancreas is sufficient. When the rupture of the canal is suspected or proved, an early laparotomy is necessary in order to investigate the pancreas and to perform the appropriate procedure. This surgery is easier before the occurrence of pseudocyst and acute pancreatitis.
Diagnostic double strike in the emergency room - two cases of complete pancreatic ruptures due to bicycle handlebar injuries on two consecutive days.

BACKGROUND: Pancreatic injuries are rare in cases of blunt abdominal trauma and therefore easily misdiagnosed at time of hospital admission. They are associated with a significantly elevated morbidity and lethality. Bicycle handlebar injuries are the most common cause of pancreatic trauma in children and adolescents. CASE PRESENTATION: We report two cases of a 23-year-old Caucasian woman and a 15-year-old Caucasian boy who presented to our clinic with a similar history of a bicycle accident on 2 consecutive days. Both suffered from a fall from a bicycle with bicycle handlebar injury 4 and 6 days prior to admission in our clinic. Emergency distal pancreatectomies were performed in both cases. CONCLUSIONS: Pancreatic injuries must be highly suspected in bicycle handlebar injuries, even if amylase/lipase levels or ultrasound findings seem unremarkable. The best initial strategies are early computed tomography and a quick referral to a level 1 trauma center. Distal pancreatectomy is the treatment of choice in cases of complete rupture of the pancreatic body.
Awareness of zoonotic diseases and parasite control practices: a survey of dog and cat owners in Qatar.

BACKGROUND: Qatar is one of the wealthiest and fastest growing economies in the world, experiencing a rapid increase in human and pet populations. Given the paucity of data on prophylactic measures against endo- and ectoparasites of pets in Qatar, as well as on the owners' awareness of zoonotic diseases, a questionnaire was conducted. METHODS: From July to November 2017, 150 multiple-choice questionnaires were administered to dog and/or cat owners who attended two veterinary clinics in Doha. RESULTS: Only 54% (81/150) owners were aware of transmittable diseases between animals and humans. " Zoonosis/zoonotic disease(s)" was unknown for 88% (132/150) of the respondents and almost a quarter had no idea of transmission pathways associated with parasitic diseases. Thirteen owners (8.7%) reported to have suffered from zoonotic diseases (10 had dermatophytosis, 2 cat-scratch disease and 1 an unknown tick-borne disease) and 24.7% had dewormed themselves. Approximately 83% had their pets yearly vaccinated and 51% identified endo- and ectoparasites on their pets. Only 10% had their animal faeces tested for intestinal parasites as requested by a veterinarian. As for internal parasite control, only 19.3% dewormed their pets with the recommended treatment regimen (minimum quarterly); 52.7% (79/150) dewormed every 4 months to 1 year; 10% (15/150) without periodicity and 8% (12/150) had never done it. For external parasite control, only 16% (24/150) treated their pets with ectoparasiticides on a monthly basis; 44.7% (67/150) every 2 months to 1 year; 6.7% (10/150) without periodicity and 24.7% (37/150) had never done it. Approximately two thirds (63.3%) of pets were allowed to sleep in the owner's bed and 60% to lick their owner's face. Almost all pets were fed with dry/canned food, but 4.7% were fed with raw meat. Approximately 79.5% of dog owners collect their pet's faeces from public areas. CONCLUSIONS: These results highlight the need to raise pet owners' awareness towards prophylactic measures to minimize the potential impact of zoonotic diseases on the health of both animals and humans in Qatar.
Astrogliosis has Different Dynamics after Cell Transplantation and Mechanical Impact in the Rodent Model of Parkinson's Disease.

BACKGROUND: Transplantation of fetal mesencephalic tissue is a well-established concept for functional reinnervation of the dopamine-depleted rat striatum. However, there is no extensive description of the glial response of the host brain following this procedure. AIMS: The present study aimed to quantitatively and qualitatively analyse astrogliosis surrounding intrastriatal grafts and compare it to the reaction to mechanical injury with the transplantation instrument only. STUDY DESIGN: Animal experimentation. METHODS: The standard 6-hydroxydopamine-induced unilateral model of Parkinson's disease was used. The experimental animals received transplantation of a single-cell suspension of E14 ventral mesencephalic tissue. Control animals (sham-transplanted) were subjected to injury by the transplantation cannula, without injection of a cell suspension. Histological analyses were carried out 7 and 28 days following the procedure by immunohistochemistry assays for tyrosine hydroxylase and glial fibrillary acidic protein. To evaluate astrogliosis, the cell density and immunopositive area were measured in distinct zones within and surrounding the grafts or the cannula tract. RESULTS: Statistical analysis revealed that astrogliosis in the grafted striatum increased from day 7 to day 28, as shown by a significant change in both cell density and the immunopositive area. The cell density increased from 816.7±370.6 to 1403±272.1 cells/mm2 (p<0.0001) аnd from 523±245.9 to 1164±304.8 cells/mm2 (p<0.0001) in the two zones in the graft core, and from 1151±218.6 to 1485±210.6 cells/mm2 (p<0.05) for the zone in the striatum immediately adjacent to the graft. The glial fibrillary acidic protein-expressing area increased from 0.3109±0.1843 to 0.7949±0.1910 (p<0.0001) and from 0.1449±0.1240 to 0.702±0.2558 (p<0.0001) for the same zones in the graft core, and from 0.5277±0.1502 to 0.6969±0.1223 (p<0.0001) for the same area adjacent to the graft zone. However, astrogliosis caused by mechanical impact only (control) did not display such dynamics. This finding suggests an influence of the grafted cells on the host's glia, possibly through cross-talk between astrocytes and transplanted neurons. CONCLUSION: This bidirectional relationship is affected by multiple factors beyond the mechanical trauma. Elucidation of these factors might help achieve better functional outcomes after intracerebral transplantation.